Collect results

Init

Imports and options

In [1]:
%load_ext autoreload
In [2]:
%autoreload 2
In [3]:
%config Application.log_level="WARN"
In [4]:
%matplotlib inline
In [5]:
import os
import sys
from glob import glob
import io
import tarfile
In [6]:
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
In [7]:
import ase
from asap3.analysis.rdf import RadialDistributionFunction

# file formats, input - output
import ase.io
from ase.io import read
from ase.io import NetCDFTrajectory

import scipy.constants as C
In [9]:
import postprocessing
In [10]:
from fireworks.utilities.filepad import FilePad 
In [11]:
fp = FilePad(
    host='localhost',
    port=27018,
    database='fireworks-jhoermann',
    username='fireworks',
    password='fireworks')
In [12]:
content, doc = fp.get_file(identifier='surfactant_on_AU_111_df_json')
In [13]:
sim_df = pd.read_json(content, orient='index')

Poster plotting

In [14]:
# matplotlib settings

# expecially for presentation, larger font settings for plotting are recommendable
SMALL_SIZE = 20
MEDIUM_SIZE = 22
BIGGER_SIZE = 26

plt.rc('font', size=MEDIUM_SIZE)          # controls default text sizes
plt.rc('axes', titlesize=MEDIUM_SIZE)     # fontsize of the axes title
plt.rc('axes', labelsize=MEDIUM_SIZE)    # fontsize of the x and y labels
plt.rc('xtick', labelsize=SMALL_SIZE)    # fontsize of the tick labels
plt.rc('ytick', labelsize=SMALL_SIZE)    # fontsize of the tick labels
plt.rc('legend', fontsize=MEDIUM_SIZE)    # legend fontsize
plt.rc('figure', titlesize=BIGGER_SIZE)  # fontsize of the figure titlex

plt.rcParams["figure.figsize"] = (16,10) # the standard figure size

plt.rcParams["lines.linewidth"] = 4
plt.rcParams["lines.markersize"] = 14
plt.rcParams["lines.markeredgewidth"]=1 

Constants and factors

Forces

$ [F_{LMP}] = \frac{ \mathrm{kcal}}{ \mathrm{mol} \cdot \mathrm{\mathring{A}}} $

$ [F_{PLT}] = \mathrm{nN}$

$ \mathrm{kcal} = 4.184 \mathrm{kJ} = 4.184 \cdot 10^{3} \mathrm{J}$

$ J = N \cdot m$

$ N = J m^{-1} = \frac{ \mathrm{kcal}}{ 4.184 \cdot 10^3 \mathrm{m} } = \frac{ \mathrm{kcal}}{ 4.184 \cdot 10^{13} \mathrm{\mathring{A}} }$

$ [F_{PLT}] = \mathrm{nN} = \frac{ 10^9 \cdot N_A^{-1}}{ 4.184 \cdot 10^{13} } \frac{\mathrm{kcal}}{\mathrm{mol} \cdot \mathrm{\mathring{A}}} = \frac{ 10^{-4} \cdot N_A^{-1}}{ 4.184 } [F_{LMP}] = 0.239 \cdot 10^{-4} N_A^{-1} [F_{LMP}] $

$ \frac{\mathrm{ kcal }}{ {\mathrm{mol} \mathrm{\mathring{A}}}} = 1.66053892103219 \cdot 10^{-11} \frac{\mathrm{J}}{\mathrm{m}}$

In [15]:
C.calorie # kCal -> kJ
Out[15]:
4.184
In [16]:
C.calorie * 1e3 # kCal -> J
Out[16]:
4184.0
In [17]:
C.calorie * 1e3 / C.angstrom # kCal / Ang -> J / m
Out[17]:
41840000000000.0
In [18]:
C.calorie * 1e3 / C.angstrom *1e9 # kCal / Ang -> n J / m = n N
Out[18]:
4.184e+22
In [19]:
force_conversion_factor = C.calorie * 1e3 / C.angstrom *1e9 / C.Avogadro# kCal / (mol * Ang ) -> n N
In [20]:
force_conversion_factor
Out[20]:
0.06947695345147255
In [21]:
# force_conversion_factor_per_mole = 1*C.calorie
In [22]:
# force_conversion_factor_per_mole
In [23]:
# force_conversion_factor_absolute = force_conversion_factor_per_mole/C.Avogadro
In [24]:
# force_conversion_factor_absolute

Constant velocity force-distance curves

In [25]:
def constant_velocity_force_distance_curve_from_thermo_ave(
    thermo_ave_out_file = None,
    thermo_out_file = None,
    initial_distance = 7.5, # nm
    total_steps = 375000,
    averaging_steps = 1000,
    dt = 2*1e-6, # ns,
    force_label         = r'$F \ [ \mathrm{nN} ]$',
    distance_label      = r'$d \ [ \mathrm{nm} ]$',
    window = 1,
    legend_prefix = None,
    interval = slice(None) ):

    # assume LAMMPS "real" units:
    # [ force ] = Kcal/mole-Angstrom
    # conversion factor to nN (nano-Newton):
    force_conversion_factor = C.calorie * 1e3 / C.angstrom *1e9 / C.Avogadro# kCal / (mol * Ang ) -> n N
    total_time = total_steps*dt
    velocity_SI = initial_distance / total_time
    
    averaging_time = averaging_steps * dt * 1e3 # ps
    
    production_thermo_pd = None
    production_thermo_ave_pd = None
    
    if thermo_out_file:
        production_thermo_pd = pd.read_csv(thermo_out_file,delim_whitespace=True)

        production_thermo_pd["distance"] = \
            initial_distance - production_thermo_pd["Step"] * velocity_SI * dt

        production_thermo_pd.set_index('distance',inplace=True)

        production_thermo_pd["indenter_non_indenter_interaction[3]"] = \
            production_thermo_pd["c_indenter_substrate_interaction[3]"] + \
            production_thermo_pd["c_indenter_surfactant_interaction[3]"] + \
            production_thermo_pd["c_indenter_solvent_interaction[3]"] + \
            production_thermo_pd["c_indenter_ion_interaction[3]"]
        plt.plot(
        force_conversion_factor*production_thermo_pd["indenter_non_indenter_interaction[3]"],
        label = "instantaneous force")
            
    if thermo_ave_out_file:
        header = pd.read_csv(thermo_ave_out_file,delim_whitespace=True,nrows=0,skiprows=1)
        columns = header.columns[1:]
        production_thermo_ave_pd = pd.read_csv( thermo_ave_out_file, delim_whitespace=True, header=None, comment='#',
            names=columns)
        production_thermo_ave_pd["distance"] = \
            initial_distance - production_thermo_ave_pd["TimeStep"] * velocity_SI * dt

        production_thermo_ave_pd.set_index('distance',inplace=True)

        production_thermo_ave_pd["indenter_non_indenter_interaction[3]"] = \
            production_thermo_ave_pd["c_indenter_substrate_interaction[3]"] + \
            production_thermo_ave_pd["c_indenter_surfactant_interaction[3]"] + \
            production_thermo_ave_pd["c_indenter_solvent_interaction[3]"] + \
            production_thermo_ave_pd["c_indenter_ion_interaction[3]"]
        plt.plot(
        force_conversion_factor*production_thermo_ave_pd["indenter_non_indenter_interaction[3]"],
        label = "{:.1f} ps average".format(averaging_time))    
   
    plt.xlabel(distance_label)
    plt.ylabel(force_label)
    plt.legend()
    return production_thermo_pd, production_thermo_ave_pd
In [26]:
def constant_velocity_force_distance_curve_from_force_file(
    force_file,
    initial_distance = 7.5, # nm
    total_steps = 375000,
    averaging_steps = 1000,
    dt = 2*1e-6, # ns,
    force_label         = r'$F \ [ \mathrm{nN} ]$',
    distance_label      = r'$d \ [ \mathrm{nm} ]$',
    window = 1,
    legend_prefix = None,
    interval = slice(None) ):

    # assume LAMMPS "real" units:
    # [ force ] = Kcal/mole-Angstrom
    # conversion factor to nN (nano-Newton):
    force_conversion_factor = C.calorie * 1e3 / C.angstrom *1e9 / C.Avogadro# kCal / (mol * Ang ) -> n N
    total_time = total_steps*dt
    velocity_SI = initial_distance / total_time
    
    averaging_time = averaging_steps * dt * 1e3 # ps
    
    indenter_forces_df = pd.read_csv(force_file,index_col=0, delim_whitespace=True) 

    indenter_forces_df["distance"] = \
        initial_distance - indenter_forces_df.index * velocity_SI * dt

    indenter_forces_df.set_index('distance',inplace=True)


    plt.plot(
        force_conversion_factor*indenter_forces_df["f_storeUnconstrainedForces"],
        label = "instantaneous force")

    plt.plot(
        force_conversion_factor*indenter_forces_df["f_storeUnconstrainedForcesAve"],
        label = "{:.1f} ps average".format(averaging_time))    
   
    plt.xlabel(distance_label)
    plt.ylabel(force_label)
    plt.legend()
    return indenter_forces_df 
In [27]:
averaging_time = 2.0
force_label         = r'$F \ [ \mathrm{nN} ]$'
distance_label      = r'$d \ [ \mathrm{nm} ]$'
In [29]:
# force distanc
thermo_df_10_m_per_s, thermo_ave_df_10_m_per_s = constant_velocity_force_distance_curve_from_thermo_ave(
    thermo_out_file = 'sandbox/10_m_per_s/joint.thermo.out',
    thermo_ave_out_file = 'sandbox/10_m_per_s/joint.thermo_ave.out',
    initial_distance = 7.5, # nm
    total_steps = 375000,
    averaging_steps = 1000 )
In [28]:
query = {
    'identifier': { '$regex': '.*indenter_forces\.txt$'},
    'metadata.surfactant':     'SDS',
    'metadata.sf_nmolecules':  646,
    'metadata.sf_preassembly': 'hemicylinders',
    'metadata.indenter_dist':  7.5}
In [29]:
files = fp.get_file_by_query(query)
In [380]:
# correction for missing entry
files[1][1]['metadata']['total_steps'] = 3750000
In [132]:
# force distanc) in files
plotData = []
for (cont,doc) in files:
    contStream = io.StringIO(cont.decode())
    plotData.append(
        constant_velocity_force_distance_curve_from_force_file(
            force_file = contStream,
            initial_distance = doc['metadata']['indenter_dist'], # nm
            total_steps = doc['metadata']['total_steps'],
            averaging_steps = 1000 ) )
In [382]:
query = {
    'identifier': { '$regex': '.*indenter_forces\.txt$'},
    'metadata.surfactant':     'SDS',
    'metadata.sf_nmolecules':  646,
    'metadata.indenter_dist':  3}
files = fp.get_file_by_query(query)
In [383]:
len(files)
Out[383]:
3
In [138]:
for 
files[0][1]['metadata']['total_steps'] = 15000000
In [131]:
# force distanc) in files
plotData = []
for (cont,doc) in files:
    contStream = io.StringIO(cont.decode())
    plotData.append(
        constant_velocity_force_distance_curve_from_force_file(
            force_file = contStream,
            initial_distance = doc['metadata']['indenter_dist'], # nm
            total_steps = doc['metadata']['total_steps'],
            averaging_steps = 1000 ) )
In [140]:
plotData[0]
Out[140]:
forces f_storeAnteSHAKEForces f_storeAnteStatForces f_storeUnconstrainedForces f_storeAnteSHAKEForcesAve f_storeAnteStatForcesAve f_storeUnconstrainedForcesAve
distance
3.000 36.4908 36.4908 36.4908 36.4908 0.00000 0.00000 0.00000
2.998 -49.0226 -49.0226 -49.0226 -49.0226 5.66622 5.66622 5.66622
2.996 267.0530 267.0530 267.0530 267.0530 -4.03088 -4.03088 -4.03088
2.994 -203.0720 -203.0720 -203.0720 -203.0720 -37.25080 -37.25080 -37.25080
2.992 281.7980 281.7980 281.7980 281.7980 -44.42220 -44.42220 -44.42220
2.990 249.0000 249.0000 249.0000 249.0000 -35.01670 -35.01670 -35.01670
2.988 -188.6160 -188.6160 -188.6160 -188.6160 20.10430 20.10430 20.10430
2.986 63.5492 63.5492 63.5492 63.5492 8.21147 8.21147 8.21147
2.984 -140.0070 -140.0070 -140.0070 -140.0070 5.18294 5.18294 5.18294
2.982 -299.6940 -299.6940 -299.6940 -299.6940 14.94310 14.94310 14.94310
2.980 247.8840 247.8840 247.8840 247.8840 8.49255 8.49255 8.49255
2.978 -164.1680 -164.1680 -164.1680 -164.1680 -19.06530 -19.06530 -19.06530
2.976 -346.6080 -346.6080 -346.6080 -346.6080 -21.33820 -21.33820 -21.33820
2.974 181.1250 181.1250 181.1250 181.1250 -3.11545 -3.11545 -3.11545
2.972 -51.7215 -51.7215 -51.7215 -51.7215 7.10673 7.10673 7.10673
2.970 330.2160 330.2160 330.2160 330.2160 -6.95233 -6.95233 -6.95233
2.968 142.7720 142.7720 142.7720 142.7720 10.19800 10.19800 10.19800
2.966 -10.0634 -10.0634 -10.0634 -10.0634 -12.75440 -12.75440 -12.75440
2.964 -121.2620 -121.2620 -121.2620 -121.2620 33.96980 33.96980 33.96980
2.962 137.0310 137.0310 137.0310 137.0310 -16.10120 -16.10120 -16.10120
2.960 -223.0850 -223.0850 -223.0850 -223.0850 -23.09250 -23.09250 -23.09250
2.958 -321.2470 -321.2470 -321.2470 -321.2470 -18.15490 -18.15490 -18.15490
2.956 35.5813 35.5813 35.5813 35.5813 -28.27010 -28.27010 -28.27010
2.954 221.3680 221.3680 221.3680 221.3680 29.06600 29.06600 29.06600
2.952 48.5570 48.5570 48.5570 48.5570 16.21880 16.21880 16.21880
2.950 78.9626 78.9626 78.9626 78.9626 4.77076 4.77076 4.77076
2.948 16.3871 16.3871 16.3871 16.3871 -1.09313 -1.09313 -1.09313
2.946 -57.8644 -57.8644 -57.8644 -57.8644 -2.60554 -2.60554 -2.60554
2.944 -13.7075 -13.7075 -13.7075 -13.7075 -10.42030 -10.42030 -10.42030
2.942 28.9488 28.9488 28.9488 28.9488 -39.30580 -39.30580 -39.30580
... ... ... ... ... ... ... ...
0.058 616.1660 616.1660 616.1660 616.1660 533.30400 533.30400 533.30400
0.056 587.3970 587.3970 587.3970 587.3970 561.83500 561.83500 561.83500
0.054 469.4660 469.4660 469.4660 469.4660 555.57700 555.57700 555.57700
0.052 491.7760 491.7760 491.7760 491.7760 511.54300 511.54300 511.54300
0.050 594.2970 594.2970 594.2970 594.2970 519.12800 519.12800 519.12800
0.048 513.8150 513.8150 513.8150 513.8150 518.91800 518.91800 518.91800
0.046 365.2820 365.2820 365.2820 365.2820 533.82000 533.82000 533.82000
0.044 346.2550 346.2550 346.2550 346.2550 499.19700 499.19700 499.19700
0.042 784.4460 784.4460 784.4460 784.4460 569.74700 569.74700 569.74700
0.040 713.0840 713.0840 713.0840 713.0840 533.59200 533.59200 533.59200
0.038 699.2660 699.2660 699.2660 699.2660 540.14400 540.14400 540.14400
0.036 353.8550 353.8550 353.8550 353.8550 576.89600 576.89600 576.89600
0.034 487.0820 487.0820 487.0820 487.0820 506.84800 506.84800 506.84800
0.032 681.0780 681.0780 681.0780 681.0780 519.00600 519.00600 519.00600
0.030 696.8800 696.8800 696.8800 696.8800 527.64500 527.64500 527.64500
0.028 437.7240 437.7240 437.7240 437.7240 571.90200 571.90200 571.90200
0.026 383.0530 383.0530 383.0530 383.0530 565.12100 565.12100 565.12100
0.024 748.1550 748.1550 748.1550 748.1550 574.34900 574.34900 574.34900
0.022 782.2470 782.2470 782.2470 782.2470 614.32900 614.32900 614.32900
0.020 619.7410 619.7410 619.7410 619.7410 576.01500 576.01500 576.01500
0.018 453.0170 453.0170 453.0170 453.0170 585.81200 585.81200 585.81200
0.016 769.1150 769.1150 769.1150 769.1150 600.97600 600.97600 600.97600
0.014 511.0540 511.0540 511.0540 511.0540 562.99000 562.99000 562.99000
0.012 423.4620 423.4620 423.4620 423.4620 585.63100 585.63100 585.63100
0.010 663.5170 663.5170 663.5170 663.5170 617.85800 617.85800 617.85800
0.008 863.1230 863.1230 863.1230 863.1230 595.88900 595.88900 595.88900
0.006 608.7120 608.7120 608.7120 608.7120 585.87600 585.87600 585.87600
0.004 748.9130 748.9130 748.9130 748.9130 600.01900 600.01900 600.01900
0.002 544.7460 544.7460 544.7460 544.7460 576.99600 576.99600 576.99600
0.000 622.9090 622.9090 622.9090 622.9090 592.41500 592.41500 592.41500

1501 rows × 7 columns

In [146]:
query = {
    'identifier': { '$regex': '.*indenter_forces\.txt$'},
    'metadata.surfactant':     'SDS',
    'metadata.sf_nmolecules':  646}
files = fp.get_file_by_query(query)
In [147]:
len(files)
Out[147]:
8
In [148]:
for i,f in enumerate(files):
    print('{:3d}:'.format(i), f[1]['identifier'],':', 'total_steps' in f[1]['metadata'])
  0: AFM/SDS/646/AU/111/52x30x2/bilayer/50Ang/stepped/30Ang/1500000/indenter_forces.txt : False
  1: AFM/SDS/646/AU/111/52x30x2/bilayer/50Ang/stepped/75Ang/3750000/indenter_forces.txt : False
  2: AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/30Ang/1500000/indenter_forces.txt : True
  3: AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/75Ang/375000/indenter_forces.txt : True
  4: AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/75Ang/3750000/indenter_forces.txt : False
  5: AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/75Ang/37500000/indenter_forces.txt : True
  6: AFM/SDS/646/AU/111/52x30x2/monolayer/50Ang/stepped/30Ang/1500000/indenter_forces.txt : True
  7: AFM/SDS/646/AU/111/52x30x2/monolayer/50Ang/stepped/75Ang/3750000/indenter_forces.txt : False
In [149]:
# wrong step size in input files
files[0][1]['metadata']['total_steps'] = 15000000 # wrong step size
files[1][1]['metadata']['total_steps'] = 37500000
files[2][1]['metadata']['total_steps'] = 1500000 # wrong step size
files[3][1]['metadata']['total_steps'] = 375000
files[4][1]['metadata']['total_steps'] = 3750000
files[5][1]['metadata']['total_steps'] = 37500000
files[6][1]['metadata']['total_steps'] = 15000000 # wrong step size
files[7][1]['metadata']['total_steps'] = 37500000
In [150]:
for f in files:
    print(f[1]['identifier'],':', f[1]['metadata']['total_steps'])
AFM/SDS/646/AU/111/52x30x2/bilayer/50Ang/stepped/30Ang/1500000/indenter_forces.txt : 15000000
AFM/SDS/646/AU/111/52x30x2/bilayer/50Ang/stepped/75Ang/3750000/indenter_forces.txt : 37500000
AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/30Ang/1500000/indenter_forces.txt : 1500000
AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/75Ang/375000/indenter_forces.txt : 375000
AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/75Ang/3750000/indenter_forces.txt : 3750000
AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/75Ang/37500000/indenter_forces.txt : 37500000
AFM/SDS/646/AU/111/52x30x2/monolayer/50Ang/stepped/30Ang/1500000/indenter_forces.txt : 15000000
AFM/SDS/646/AU/111/52x30x2/monolayer/50Ang/stepped/75Ang/3750000/indenter_forces.txt : 37500000
In [151]:
# force distanc) in files
plotData = []
for (cont,doc) in files:
    contStream = io.StringIO(cont.decode())
    plotData.append(
        constant_velocity_force_distance_curve_from_force_file(
            force_file = contStream,
            initial_distance = doc['metadata']['indenter_dist'], # nm
            total_steps = doc['metadata']['total_steps'],
            averaging_steps = 1000 ) )
In [152]:
for i,f in enumerate(files):
    print('{:3d}:'.format(i), f[1]['identifier'],':', 'total_steps' in f[1]['metadata'])
  0: AFM/SDS/646/AU/111/52x30x2/bilayer/50Ang/stepped/30Ang/1500000/indenter_forces.txt : True
  1: AFM/SDS/646/AU/111/52x30x2/bilayer/50Ang/stepped/75Ang/3750000/indenter_forces.txt : True
  2: AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/30Ang/1500000/indenter_forces.txt : True
  3: AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/75Ang/375000/indenter_forces.txt : True
  4: AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/75Ang/3750000/indenter_forces.txt : True
  5: AFM/SDS/646/AU/111/52x30x2/hemicylinders/50Ang/stepped/75Ang/37500000/indenter_forces.txt : True
  6: AFM/SDS/646/AU/111/52x30x2/monolayer/50Ang/stepped/30Ang/1500000/indenter_forces.txt : True
  7: AFM/SDS/646/AU/111/52x30x2/monolayer/50Ang/stepped/75Ang/3750000/indenter_forces.txt : True
In [114]:
files_hemicylinders = files[2:6]
In [115]:
files_1m_per_s = [ files[6], files[0], files[2] ] 
In [116]:
files_10cm_per_s = [ files[7], files[1], files[5] ] 
In [153]:
plotData_hemicylinders = [ plotData[5], plotData[4], plotData[2], plotData[3] ]
In [154]:
plotData_1m_per_s = [ plotData[6], plotData[0], plotData[2] ] 
In [155]:
plotData_10cm_per_s = [ plotData[7], plotData[1], plotData[5] ] 
In [156]:
labels =  [ 
    r'$1 \mathrm{\ m \ s^{-1}}$, bilayer',
    r'$10 \mathrm{\ m \ s^{-1}}$, hemicylinder',    
    r'$1 \mathrm{\ m \ s^{-1}}$, hemicylinder',
    r'$0.1 \mathrm{\ m \ s^{-1}}$, hemicylinder',
    r'$1 \mathrm{\ m \ s^{-1}}$, bilayer']   
In [157]:
labels_hemicylinders =  [ 
    r'$0.1 \mathrm{\ m \ s^{-1}}$',
    r'$1 \mathrm{\ m \ s^{-1}}$',
    r'$1 \mathrm{\ m \ s^{-1}}$',
    r'$10 \mathrm{\ m \ s^{-1}}$']
In [158]:
labels_1m_per_s = [ 
    'monolayer',    
    'bilayer',
    'hemicylinder' ]
In [159]:
plt.rcParams["figure.figsize"] = (8,6) # the standard figure size
In [160]:
plt.plot(
    force_conversion_factor*plotData_hemicylinders[0]["f_storeUnconstrainedForcesAve"][
            (0.0 < plotData_hemicylinders[0].index) & (plotData_hemicylinders[0].index < 7.0)].rolling(window=1,center=True).mean(),
    label = lab) 
Out[160]:
[<matplotlib.lines.Line2D at 0x7f13d267def0>]
In [161]:
figure = plt.figure()
windows = np.array([1,1,10,1]) # do average on the same scale, i.e. 2ps
for (dat,lab,win) in zip(plotData_hemicylinders,labels_hemicylinders,windows):
    plt.plot(
        force_conversion_factor*dat["f_storeUnconstrainedForcesAve"][
                (0.0 < dat.index) & (dat.index < 7.0)].rolling(window=win,center=True).mean(),
        label = lab, ls=':') 
plt.xlabel(distance_label)
plt.ylabel(force_label)
#plt.legend(frameon=False,ncol=2)
#plt.tight_layout(pad=1)
legend = plt.legend(frameon=False,loc='center right')
renderer = figure.canvas.get_renderer()
# get the width of your widest label, since every label will need 
# to shift by this amount after we align to the right
shift = max([t.get_window_extent(renderer).width for t in legend.get_texts()])
for t in legend.get_texts():
    t.set_ha('right') # ha is alias for horizontalalignment
    t.set_position((shift,0))
In [162]:
# get the width of your widest label, since every label will need 
# to shift by this amount after we align to the right

shift = max([t.get_window_extent().width for t in legend.get_texts()])
for t in legend.get_texts():
    t.set_ha('right') # ha is alias for horizontalalignment
    t.set_position((shift,0))
In [163]:
legend.get_texts()[0].get_window_extent().width
Out[163]:
105.65536494140622
In [164]:
# get the width of your widest label, since every label will need 
# to shift by this amount after we align to the right
shift = max([t.get_window_extent().width for t in legend.get_texts()])
for t in legend.get_texts():
    t.set_ha('right') # ha is alias for horizontalalignment
    t.set_position((shift,0))

1m per s approach

In [165]:
windows = np.array([10,10,10,]) # do average on the same scale, i.e. 2ps
for (dat,lab,win) in zip(plotData_1m_per_s,labels_1m_per_s,windows):
    plt.plot(
        force_conversion_factor*dat["f_storeUnconstrainedForcesAve"].rolling(window=win,center=True).mean(),
        label = lab) 

plt.xlabel(distance_label)
plt.ylabel(force_label)
plt.legend()
Out[165]:
<matplotlib.legend.Legend at 0x7f13d8058a20>

10 cm per s approach

In [166]:
windows = np.array([10,10,10,]) # do average on the same scale, i.e. 2ps
for (dat,lab,win) in zip(plotData_10cm_per_s,labels_1m_per_s,windows):
    plt.plot(
        force_conversion_factor*dat["f_storeUnconstrainedForcesAve"].rolling(window=win,center=True).mean(),
        label = lab) 

plt.xlabel(distance_label)
plt.ylabel(force_label)
plt.legend()
Out[166]:
<matplotlib.legend.Legend at 0x7f13d263e6d8>
In [178]:
test = None
In [179]:
type(test) is not list
Out[179]:
True
In [180]:
test = [None]
In [181]:
test
Out[181]:
[None]
In [182]:
type(test) is not list
Out[182]:
False
In [167]:
windows = np.array([10,10,10]) # do average on the same scale, i.e. 2*2ps
for (dat,lab,win) in zip(plotData_1m_per_s,labels_1m_per_s,windows):
    plt.plot(
        force_conversion_factor*dat[
            "f_storeUnconstrainedForcesAve"][
                (0.0 < dat.index) & (dat.index < 4.0)].rolling(window=win,center=True).mean(),
        label = lab) 
plt.xlabel(distance_label)
plt.ylabel(force_label)
plt.legend()
Out[167]:
<matplotlib.legend.Legend at 0x7f13d2648978>
In [169]:
windows = np.array([10,10,1,]) # do average on the same scale, i.e. 2*2ps
for (dat,lab,win) in zip(plotData_1m_per_s,labels_1m_per_s,windows):
    plt.plot(
        force_conversion_factor*dat[
            "f_storeUnconstrainedForcesAve"][
                (0.0 < dat.index) & (dat.index < 3.0)].rolling(window=win,center=True).mean(),
        label = lab) 
plt.xlabel(distance_label)
plt.ylabel(force_label)
plt.legend()
Out[169]:
<matplotlib.legend.Legend at 0x7f13daf6b080>
In [70]:
# force distanc
indenter_forces_10_m_per_s = constant_velocity_force_distance_curve_from_force_file(
    force_file = contStream[0],
    initial_distance = doc[0]['metadata']['indenter_dist'], # nm
    total_steps = doc[0]['metadata']['total_steps'],
    averaging_steps = 1000 )
In [50]:
# force distanc
indenter_forces_10_m_per_s = constant_velocity_force_distance_curve_from_force_file(
    force_file = './sandbox/10_m_per_s/indenter_z_forces.txt',
    initial_distance = 7.5, # nm
    total_steps = 375000,
    averaging_steps = 1000 )
In [32]:
# force distanc
indenter_forces_1_m_per_s = constant_velocity_force_distance_curve_from_force_file(
    force_file = './sandbox/1_m_per_s/indenter_z_forces.txt',
    initial_distance = 7.5, # nm
    total_steps = 3750000,
    averaging_steps = 10000 )
In [33]:
indenter_forces_1_m_per_s.head()
Out[33]:
forces f_storeAnteSHAKEForces f_storeAnteStatForces f_storeUnconstrainedForces f_storeAnteSHAKEForcesAve f_storeAnteStatForcesAve f_storeUnconstrainedForcesAve
distance
7.50 102.2570 102.2570 102.2570 102.2570 0.0000 0.0000 0.0000
7.48 -174.9440 -174.9440 -174.9440 -174.9440 22.8667 22.8667 22.8667
7.46 -26.2528 -26.2528 -26.2528 -26.2528 36.4658 36.4658 36.4658
7.44 -134.9060 -134.9060 -134.9060 -134.9060 37.3810 37.3810 37.3810
7.42 45.3743 45.3743 45.3743 45.3743 49.5057 49.5057 49.5057
In [37]:
plt.plot(force_conversion_factor*indenter_forces_1_m_per_s["f_storeUnconstrainedForcesAve"],
        label = r'$1 \mathrm{\ m \ s^{-1}}$') 
plt.plot(force_conversion_factor*indenter_forces_10_m_per_s["f_storeUnconstrainedForcesAve"],
        label = r'$10 \mathrm{\ m \ s^{-1}}$')       
plt.xlabel(distance_label)
plt.ylabel(force_label)
plt.legend()
Out[37]:
<matplotlib.legend.Legend at 0x7fb3184cfb38>
In [44]:
# force distanc
nonindenter_forces_10_m_per_s = constant_velocity_force_distance_curve_from_force_file(
    force_file = './sandbox/10_m_per_s/nonindenter_z_forces.txt',
    initial_distance = 7.5, # nm
    total_steps = 375000,
    averaging_steps = 1000 )
In [67]:
thermo_ave_df_1_m_per_s = [None]*2
In [46]:
 thermo_df_1_m_per_s, thermo_ave_df_1_m_per_s = constant_velocity_force_distance_curve_from_thermo_ave(
    thermo_ave_out_file = 'sandbox/1_m_per_s/thermo_ave.out',
    thermo_out_file = 'sandbox/1_m_per_s/thermo.out',
    initial_distance = 7.5, # nm
    total_steps = 3750000,
    averaging_steps = 1000 )
In [69]:
_, thermo_ave_df_1_m_per_s[1] = constant_velocity_force_distance_curve(
    thermo_ave_out_file = 'sandbox/1_m_per_s/thermo_ave.out.3',
    initial_distance = 7.5, # nm
    total_steps = 3750000,
    averaging_steps = 1000 )
In [100]:
plt.plot(force_conversion_factor*thermo_ave_df_1_m_per_s[0]["indenter_non_indenter_interaction[3]"].loc[ thermo_ave_df_1_m_per_s[0].index < 7],
        label='instantaneous force')
plt.plot(force_conversion_factor*thermo_ave_df_1_m_per_s[1]["indenter_non_indenter_interaction[3]"],
        label = "{:.1f} ps average".format(averaging_time))    
   
plt.xlabel(distance_label)
plt.ylabel(force_label)
plt.legend()
Out[100]:
<matplotlib.legend.Legend at 0x7f9e90449eb8>
In [115]:
plt.plot(force_conversion_factor*thermo_ave_df_1_m_per_s[0]["c_indenter_surfactant_interaction[3]"])
plt.plot(force_conversion_factor*thermo_ave_df_10_m_per_s["c_indenter_surfactant_interaction[3]"] )
Out[115]:
[<matplotlib.lines.Line2D at 0x7f9e88e7df60>]
In [121]:
plt.plot(force_conversion_factor*thermo_ave_df_1_m_per_s[0]["indenter_non_indenter_interaction[3]"].loc[ thermo_ave_df_1_m_per_s[0].index < 7 ],
        label = r'$1 \mathrm{\ m \ s^{-1}}$') 
plt.plot(force_conversion_factor*thermo_ave_df_1_m_per_s[1]["indenter_non_indenter_interaction[3]"].loc[ thermo_ave_df_1_m_per_s[1].index < 7 ])
plt.plot(force_conversion_factor*thermo_ave_df_10_m_per_s["indenter_non_indenter_interaction[3]"].loc[ (7 > thermo_ave_df_10_m_per_s.index) & (thermo_ave_df_10_m_per_s.index > 3) ],
                label = r'$10 \mathrm{\ m \ s^{-1}}$')    
   
plt.xlabel(distance_label)
plt.ylabel(force_label)
plt.legend()
Out[121]:
<matplotlib.legend.Legend at 0x7f9e88b3d7f0>

Drag force away from surface

in nN

1 m / s

In [126]:
(force_conversion_factor*thermo_ave_df_1_m_per_s[0]["indenter_non_indenter_interaction[3]"].loc[ 
        (thermo_ave_df_1_m_per_s[0].index > 4) & (thermo_ave_df_1_m_per_s[0].index < 7) ]).mean()
Out[126]:
0.26009859871139096

10 m / s

In [127]:
(force_conversion_factor*thermo_ave_df_10_m_per_s["indenter_non_indenter_interaction[3]"].loc[
        (thermo_ave_df_10_m_per_s.index > 4) & (thermo_ave_df_10_m_per_s.index < 7) ]).mean()
Out[127]:
2.470797203694911

File system

In [526]:
lmplab_prefix = os.getcwd()
In [527]:
lmplab_prefix
Out[527]:
'/work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab'
In [528]:
sds_sys_subdir = os.sep.join(('sds','201810','sys'))
In [529]:
sds_sys_subdir
Out[529]:
'sds/201810/sys'
In [530]:
ctab_sys_subdir = os.sep.join(('ctab','201809','sys'))
In [531]:
ctab_sys_subdir
Out[531]:
'ctab/201809/sys'
In [532]:
ctab_absolute_prefix = os.sep.join((lmplab_prefix,ctab_sys_subdir))
In [533]:
sds_absolute_prefix = os.sep.join((lmplab_prefix,sds_sys_subdir))
In [534]:
sds_absolute_prefix
Out[534]:
'/work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys'
In [535]:
indenter_system_suffix = '_50Ang_stepped'
In [536]:
ctab_system_glob_pattern = ''.join((
    ctab_absolute_prefix,os.sep,'*',indenter_system_suffix))
In [537]:
sds_system_glob_pattern = ''.join((
    sds_absolute_prefix,os.sep,'*',indenter_system_suffix))
In [538]:
ctab_system_glob_pattern = ''.join((
    ctab_absolute_prefix,os.sep,'*',indenter_system_suffix))
In [539]:
sds_system_glob_pattern
Out[539]:
'/work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/*_50Ang_stepped'
In [540]:
ctab_system_glob_pattern
Out[540]:
'/work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/*_50Ang_stepped'
In [541]:
# os.chdir(absolute_prefix)
In [542]:
sds_indenter_system_absolute_prefix_lst = sorted(glob(sds_system_glob_pattern))
In [543]:
ctab_indenter_system_absolute_prefix_lst = sorted(glob(ctab_system_glob_pattern))
In [544]:
sds_indenter_system_lst = [ 
    os.path.basename(
        indenter_system_absolute_prefix) for indenter_system_absolute_prefix
            in sds_indenter_system_absolute_prefix_lst ]
In [545]:
ctab_indenter_system_lst = [ 
    os.path.basename(
        indenter_system_absolute_prefix) for indenter_system_absolute_prefix
            in ctab_indenter_system_absolute_prefix_lst ]
In [588]:
ctab_indenter_system_lst
Out[588]:
['1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '415_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '515_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '515_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped']
In [589]:
sds_indenter_system_lst
Out[589]:
['1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_hemicylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped']
In [548]:
system_lst = [*sds_indenter_system_lst, *ctab_indenter_system_lst]
In [549]:
system_absolute_prefix_lst = [*sds_indenter_system_absolute_prefix_lst, 
                              *ctab_indenter_system_absolute_prefix_lst]
In [550]:
system_absolute_prefix_dict = dict(zip( system_lst, system_absolute_prefix_lst))
In [551]:
sorted(system_absolute_prefix_dict)
Out[551]:
['1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '415_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '515_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '515_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_hemicylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped']
In [552]:
production_steps = [500000, 1000000]
In [590]:
production_steps
Out[590]:
[500000, 1000000]
In [554]:
production_subdir_lst = [ 'production_{:d}'.format(steps) for steps in production_steps]
In [591]:
production_subdir_lst
Out[591]:
['production_500000', 'production_1000000']
In [556]:
production_dict = dict( zip(production_steps, production_subdir_lst) )
In [592]:
production_dict
Out[592]:
{500000: 'production_500000', 1000000: 'production_1000000'}
In [594]:
system_names = system_lst
In [595]:
system_names
Out[595]:
['1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_hemicylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '415_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '515_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '515_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped']
In [596]:
os.getcwd()
Out[596]:
'/work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab'
In [597]:
indenter_dict = {system: [] for system in system_names}

Extract colvars tar files

In [598]:
# unpack all tar files
for system_name in system_names:
    system_absolute_prefix = system_absolute_prefix_dict[system_name]
    print("{:s}: {:s}".format(system_name, system_absolute_prefix))
    
    for steps, production_subdir in production_dict.items():
        production_absolute_prefix = os.sep.join((
            system_absolute_prefix, production_subdir))
        if os.path.isdir(production_absolute_prefix):
            print("  {:s}/{:s} exists.".format(system_name, production_subdir))
            tarfile_glob_pattern = os.sep.join((
                production_absolute_prefix,'*.tar.gz'))
            tarfiles = glob(tarfile_glob_pattern)
            if len(tarfiles) > 0:
                print("    {:s}/{:s} has {:s}.".format(
                    system_name, production_subdir, tarfiles[0]))
                colvars_tar = tarfile.open(tarfiles[0], 'r')
                print("    Content: {}".format(colvars_tar.getnames()))
                colvars_tar.extractall(path=production_absolute_prefix)
                print("    Extracted.")
                indenter_dict[system_name].append(steps)
1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000 exists.
    1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.colvars.traj', '1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.colvars.state', '1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.restart1.colvars.state', '1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000 exists.
    129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.colvars.traj', '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.colvars.state', '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.restart1.colvars.state', '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000 exists.
    220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.colvars.traj', '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.colvars.state', '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.restart1.colvars.state', '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000 exists.
    220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.colvars.traj', '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.colvars.state', '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.restart1.colvars.state', '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000 exists.
    377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.colvars.traj', '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.colvars.state', '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.restart1.colvars.state', '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
377_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped
377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000 exists.
    377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.colvars.traj', '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.colvars.state', '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.restart1.colvars.state', '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000 exists.
    646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.colvars.traj', '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.colvars.state', '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.restart1.colvars.state', '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped
  646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped/production_500000 exists.
    646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped.colvars.traj', '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped.colvars.state', '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped.restart1.colvars.state', '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
646_SDS_on_AU_111_51x30x2_hemicylinders_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_hemicylinders_with_counterion_50Ang_stepped
646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000 exists.
    646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.colvars.traj', '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.colvars.state', '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.restart1.colvars.state', '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000 exists.
    75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.colvars.traj', '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.colvars.state', '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.restart1.colvars.state', '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000 exists.
    75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.colvars.traj', '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.colvars.state', '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.restart1.colvars.state', '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
  1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000 exists.
    1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/colvars.tar.gz.
    Content: ['1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.colvars.traj', '1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.restart1.colvars.state', '1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
  1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000 exists.
    1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/colvars.tar.gz.
    Content: ['1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.colvars.traj', '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.restart1.colvars.state', '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
  1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000 exists.
    1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.colvars.traj', '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.colvars.state', '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.restart1.colvars.state', '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
  367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000 exists.
    367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.colvars.traj', '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.colvars.state', '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.restart1.colvars.state', '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
415_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/415_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped
515_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/515_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
515_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/515_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped
653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
  653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000 exists.
    653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.colvars.traj', '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.colvars.state', '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.restart1.colvars.state', '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
  653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000 exists.
    653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/colvars.tar.gz.
    Content: ['653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.colvars.traj', '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.colvars.state', '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.restart1.colvars.state', '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped
  653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped/production_500000 exists.
    653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.colvars.traj', '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.colvars.state', '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.restart1.colvars.state', '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
  653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped/production_1000000 exists.
    653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped/production_1000000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped/production_1000000/colvars.tar.gz.
    Content: ['653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.colvars.traj', '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.colvars.state', '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.restart1.colvars.state', '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
  653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000 exists.
    653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000/colvars.tar.gz.
    Content: ['653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.colvars.traj', '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.colvars.state', '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.restart1.colvars.state', '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
  653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000 exists.
    653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000 has /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/colvars.tar.gz.
    Content: ['653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.colvars.traj', '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.restart1.colvars.state', '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count', '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad', '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf']
    Extracted.
In [600]:
indenter_dict
Out[600]:
{'1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': [1000000],
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped': [1000000],
 '1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': [500000],
 '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': [500000],
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped': [500000],
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '377_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped': [],
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': [500000],
 '415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': [],
 '415_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped': [],
 '515_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': [],
 '515_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped': [],
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped': [500000],
 '646_SDS_on_AU_111_51x30x2_hemicylinders_with_counterion_50Ang_stepped': [],
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': [500000],
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': [500000,
  1000000],
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped': [500000,
  1000000],
 '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped': [500000,
  1000000],
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': [500000]}
In [864]:
indenter_dict
Out[864]:
{'1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': [1000000],
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped': [1000000],
 '1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': [500000],
 '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': [500000],
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped': [500000],
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '377_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped': [],
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': [500000],
 '415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': [],
 '415_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped': [],
 '515_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': [],
 '515_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped': [],
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped': [500000],
 '646_SDS_on_AU_111_51x30x2_hemicylinders_with_counterion_50Ang_stepped': [],
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': [500000],
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': [500000,
  1000000],
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped': [500000,
  1000000],
 '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped': [500000,
  1000000],
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': [500000],
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': [500000]}

Batch

In [601]:
system_names = [ system_name for system_name, run_list \
                 in indenter_dict.items() if len(run_list) > 0 ]
In [602]:
set(system_names) & set(sds_indenter_system_lst)
Out[602]:
{'1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped'}
In [603]:
set(system_names) & set(ctab_indenter_system_lst)
Out[603]:
{'1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped'}

Read data files

In [994]:
# read all systems
i = 0
#df_dict = {}
for system_name in system_names:
    system_absolute_prefix = system_absolute_prefix_dict[system_name]
    print("{:s}: {:s}".format(system_name, system_absolute_prefix))

    #df_dict[system_name] = {}
    if system_name not in df_dict:
        df_dict[system_name] = {}
        
    for total_steps in indenter_dict[system_name]:
        if exclude_dict and system_name in exclude_dict and total_steps in exclude_dict[system_name]:
            continue # skip system
            
        production_absolute_prefix = os.sep.join((
            system_absolute_prefix, production_dict[total_steps]))
        #os.chdir( production_dict[total_steps] )
        print("{:3d}: {:s}".format(i,production_absolute_prefix))
        
        df_dict[system_name][total_steps] = {}
        df_dict[system_name][total_steps]['colvars'] = \
            postprocessing.read_colvars_traj(
                prefix = production_absolute_prefix )
            
        ( df_dict[system_name][total_steps]['ti.pmf'],
          df_dict[system_name][total_steps]['ti.grad'],
          df_dict[system_name][total_steps]['ti.count'] ) = \
            postprocessing.read_colvars_ti( 
                prefix = production_absolute_prefix )
            
        df_dict[system_name][total_steps]['thermo'] = \
            postprocessing.read_production_thermo(
                prefix = production_absolute_prefix )

        i+=1
1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  0: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000
129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  1: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000
220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  2: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000
220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  3: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000
377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  4: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000
377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  5: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000
646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  6: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000
646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped
  7: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped/production_500000
646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  8: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000
75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  9: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000
75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
 10: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000
1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
 11: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000
367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
 12: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000
653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
 13: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000
 14: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000
653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped
 15: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped/production_500000
653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
 16: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000

Read forces from netcdf

In [569]:
force_keys = [
    'forces', 
    'f_storeAnteSHAKEForces', 
    'f_storeAnteStatForces', 
    'f_storeUnconstrainedForces', 
    'f_storeAnteSHAKEForcesAve', 
    'f_storeAnteStatForcesAve', 
    'f_storeUnconstrainedForcesAve' ]
In [570]:
t2n_array_dict = { system_name: postprocessing.sds_t2n_array for system_name
                      in sds_indenter_system_lst }
In [571]:
t2n_array_dict.update( 
    { system_name: postprocessing.ctab_t2n_array for system_name
                      in ctab_indenter_system_lst } )
In [882]:
# 
exclude_dict = {'1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': [1000000],
                '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped': [1000000],
                '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped': [1000000],
                '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped': [1000000],}
               #'653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped':[1000000]} # done, but not fully concatenated yet
# 1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000
In [884]:
indenter_dict['653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped']
Out[884]:
[500000, 1000000]
In [885]:
constant_offset = 7.0637 # Ang, half thickness of substrate
In [1005]:
# RUN AGAIN
# read all systems
i = 0
# update df_dict
for system_name in system_names:
    system_absolute_prefix = system_absolute_prefix_dict[system_name]
    print("{:s}: {:s}".format(system_name, system_absolute_prefix))

    if system_name not in df_dict: # this should never be the case if data files have been read precedingly
        df_dict[system_name] = {}
        
    t2n_array = t2n_array_dict[system_name]
    
    for total_steps in indenter_dict[system_name]:
        if exclude_dict and system_name in exclude_dict and total_steps in exclude_dict[system_name]:
            continue # skip system
            
        production_absolute_prefix = os.sep.join((
            system_absolute_prefix, production_dict[total_steps]))
        #os.chdir( production_dict[total_steps] )
        print("{:3d}: {:s}".format(i,production_absolute_prefix))
        
        # check whether has been processed before:
        system_prefix = system_name + '_' + production_dict[total_steps]
        indenter_z_forces_json_name = system_prefix + '_indenter_z_forces.json'
        nonindenter_z_forces_json_name = system_prefix + '_nonindenter_z_forces.json'
        indenter_z_forces_json_absolute_file_name = os.sep.join((
            production_absolute_prefix,indenter_z_forces_json_name))
        nonindenter_z_forces_json_absolute_file_name = os.sep.join((
            production_absolute_prefix,nonindenter_z_forces_json_name))
    
        
        netcdf_glob_pattern = os.sep.join((
            production_absolute_prefix, '*.nc'))

        netcdf = glob(netcdf_glob_pattern)[0]

        tmp_traj = NetCDFTrajectory(netcdf, 'r', 
            types_to_numbers = list( t2n_array ),
            keep_open=True )
        
        # use first frame to crudely identify indenter
        solid_selection = (
            tmp_traj[0].get_atomic_numbers() == ase.data.atomic_numbers['Au'])
        indenter_selection = (
            solid_selection & (tmp_traj[0].get_positions()[:,2] > 20 ) ) 
        # 20 some arbitrary xy-plane seperating substrate & indenter
        
        print("solid: {: 9d} atoms, therof indenter: {: 9d} atoms.".format(
            np.count_nonzero(solid_selection),
            np.count_nonzero(indenter_selection) ) )
        
        # derive z dist offset
        # (COM-COM distance is stored, we want surface-apex distance)
        #pmf_df = df_dict[system_name][total_steps]['ti.pmf']
        colvars_traj_df = df_dict[system_name][total_steps]['colvars']
        #thermo_df = df_dict[system_name][total_steps]['thermo']
        
        # initial apex position at frame 0:
        apex_z0 = tmp_traj[0][indenter_selection].get_positions()[:,2].min()

        # initial substrate surface position at frame 0:
        surface_z0 = tmp_traj[0][solid_selection # in order to have a standardized width
            & ~indenter_selection].get_positions()[:,2].mean() + constant_offset

        extents_dist_0 = apex_z0 - surface_z0
        com_com_dist_0 = colvars_traj_df.loc[0,'com_com_dist_z']
        dist_offset = com_com_dist_0 - extents_dist_0
        
        print("initial com-com dist:        {:8.3f}".format(com_com_dist_0) )
        print("initial apex-surface dist:   {:8.3f}".format(extents_dist_0) )
        print("resulting positional offset: {:8.3f}".format(dist_offset) )
        
        
        # sum forces on all indenter atoms for all frames
        if os.path.isfile(indenter_z_forces_json_absolute_file_name) and \
            os.path.isfile(nonindenter_z_forces_json_absolute_file_name):
            print("Has been processed before, reading json files {:s} and {:s}.".format(
                indenter_z_forces_json_absolute_file_name,
                nonindenter_z_forces_json_absolute_file_name))
            indenter_force_z_sum_df = pd.read_json(
                indenter_z_forces_json_absolute_file_name, orient='index')
            nonindenter_force_z_sum_df = pd.read_json(
                nonindenter_z_forces_json_absolute_file_name, orient='index')
        else:
            print("Reading NetCDF.")
            indenter_force_sum_dict = { key: [] for key in force_keys }
            nonindenter_force_sum_dict = { key: [] for key in force_keys }
            for key in force_keys:    
                if key in tmp_traj[0].arrays:
                    indenter_force_sum_dict[key] = np.array(
                        [ f[indenter_selection].arrays[key].sum(axis=0) 
                             for f in tmp_traj ] )
                    nonindenter_force_sum_dict[key] = np.array(
                        [ f[~indenter_selection].arrays[key].sum(axis=0) 
                             for f in tmp_traj ] )
                else:
                    print("Warning: key '{:s}' not in NetCDF".format(key))

            # only keep z forces and create data frames
            indenter_force_z_sum_dict = { key: value[:,2] for key, value 
                            in indenter_force_sum_dict.items() }

            nonindenter_force_z_sum_dict = { key: value[:,2] for key, value 
                                    in nonindenter_force_sum_dict.items() }

            indenter_force_z_sum_df = pd.DataFrame.from_dict(
                indenter_force_z_sum_dict, dtype=float)

            nonindenter_force_z_sum_df = pd.DataFrame.from_dict(
                nonindenter_force_z_sum_dict, dtype=float)

            # make indices agree
            netcdf_output_interval = colvars_traj_df.index[-1]/(len(tmp_traj)-1)
            print("netcdf stores every {:d}th of {:d} frames in total.".format(
                int(netcdf_output_interval), int(colvars_traj_df.index[-1]) ) )

            indenter_force_z_sum_df.set_index(
                (indenter_force_z_sum_df.index*netcdf_output_interval).astype(int),
                inplace=True )
            nonindenter_force_z_sum_df.set_index(
                (nonindenter_force_z_sum_df.index*netcdf_output_interval).astype(int),
                inplace=True )
        
            # store z forces in json files
            indenter_force_z_sum_df.to_json(
                indenter_z_forces_json_absolute_file_name,  orient='index')

            nonindenter_force_z_sum_df.to_json(
                nonindenter_z_forces_json_absolute_file_name,  orient='index')

        # keep forces in data frame dict
        if total_steps not in df_dict[system_name]: 
            # this should never be the case if data files have been read precedingly
            df_dict[system_name][total_steps] = {}
        
        df_dict[system_name][total_steps]['indenter_forces_z'] = \
            indenter_force_z_sum_df
            
        df_dict[system_name][total_steps]['nonindenter_forces_z'] = \
            nonindenter_force_z_sum_df
            
        df_dict[system_name][total_steps]['dist_offset'] = dist_offset

        i+=1
1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  0: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000
solid:     21901 atoms, therof indenter:      3541 atoms.
initial com-com dist:         127.183
initial apex-surface dist:     97.459
resulting positional offset:   29.724
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  1: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000
solid:     21901 atoms, therof indenter:      3541 atoms.
initial com-com dist:         127.338
initial apex-surface dist:     97.626
resulting positional offset:   29.711
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  2: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000
solid:     21901 atoms, therof indenter:      3541 atoms.
initial com-com dist:         127.310
initial apex-surface dist:     97.595
resulting positional offset:   29.716
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  3: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000
solid:     21901 atoms, therof indenter:      3541 atoms.
initial com-com dist:         127.238
initial apex-surface dist:     97.528
resulting positional offset:   29.710
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  4: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000
solid:     21901 atoms, therof indenter:      3541 atoms.
initial com-com dist:         127.097
initial apex-surface dist:     97.376
resulting positional offset:   29.721
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  5: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000
solid:     21901 atoms, therof indenter:      3541 atoms.
initial com-com dist:         127.217
initial apex-surface dist:     97.501
resulting positional offset:   29.716
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  6: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000
solid:     21901 atoms, therof indenter:      3541 atoms.
initial com-com dist:         127.099
initial apex-surface dist:     97.384
resulting positional offset:   29.714
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped
  7: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped/production_500000
solid:     21901 atoms, therof indenter:      3541 atoms.
initial com-com dist:         127.178
initial apex-surface dist:     97.438
resulting positional offset:   29.740
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped/production_500000/646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped/production_500000/646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
  8: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000
solid:     21901 atoms, therof indenter:      3541 atoms.
initial com-com dist:         127.233
initial apex-surface dist:     97.517
resulting positional offset:   29.716
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped
  9: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000
solid:     21901 atoms, therof indenter:      3541 atoms.
initial com-com dist:         127.120
initial apex-surface dist:     97.408
resulting positional offset:   29.712
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped/production_500000/75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped
 10: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000
solid:     21901 atoms, therof indenter:      3541 atoms.
initial com-com dist:         127.196
initial apex-surface dist:     97.479
resulting positional offset:   29.718
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
 11: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000
solid:     29953 atoms, therof indenter:      3184 atoms.
initial com-com dist:         122.942
initial apex-surface dist:    119.029
resulting positional offset:    3.913
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
 12: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000
solid:     30145 atoms, therof indenter:      2932 atoms.
initial com-com dist:         145.056
initial apex-surface dist:    118.984
resulting positional offset:   26.072
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000/367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000/367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
 13: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000
solid:     29953 atoms, therof indenter:      2737 atoms.
initial com-com dist:         143.716
initial apex-surface dist:    118.645
resulting positional offset:   25.070
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_500000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
 14: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000
solid:     29953 atoms, therof indenter:      2737 atoms.
initial com-com dist:         143.716
initial apex-surface dist:    118.645
resulting positional offset:   25.070
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_1000000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_1000000_nonindenter_z_forces.json.
653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped
 15: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped/production_500000
solid:     30145 atoms, therof indenter:      2929 atoms.
initial com-com dist:         144.622
initial apex-surface dist:    118.377
resulting positional offset:   26.245
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped/production_500000/653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped/production_500000/653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
 16: /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000
solid:     30145 atoms, therof indenter:      2934 atoms.
initial com-com dist:         145.102
initial apex-surface dist:    119.140
resulting positional offset:   25.962
Has been processed before, reading json files /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_500000_indenter_z_forces.json and /work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/ctab/201809/sys/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_500000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_500000_nonindenter_z_forces.json.
In [893]:
tmp_traj[1]
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-893-983d7d83670c> in <module>()
----> 1 tmp_traj[1]

/work/ws/nemo/fr_lp1029-IMTEK_SIMULATION-0/local_modules/ase/3.15.0/lib/python3.6/site-packages/ase-3.15.0-py3.6.egg/ase/io/netcdftrajectory.py in __getitem__(self, i)
    604         if i < 0 or i >= N:
    605             self._close()
--> 606             raise IndexError('Trajectory index out of range.')
    607         return self[i]
    608 

IndexError: Trajectory index out of range.
In [766]:
df_dict['1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped'][500000].keys()
Out[766]:
dict_keys(['colvars', 'ti.pmf', 'ti.grad', 'ti.count', 'thermo', 'indenter_forces_z', 'nonindenter_forces_z', 'dist_offset'])

Make plots

In [863]:
system_names
Out[863]:
['1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped']
In [621]:
import re
In [623]:
bilayer_regex = re.compile('.*bilayer.*')
In [633]:
monolayer_regex = re.compile('.*monolayer.*')
In [648]:
cylinders_regex = re.compile('(?!hemi)*cylinders.*')
In [695]:
hemicylinders_regex = re.compile('.*hemicylinders.*')
In [696]:
sds_regex = re.compile('.*SDS.*')
In [697]:
ctab_regex = re.compile('.*CTAB.*')
In [698]:
ctab_653_regex = re.compile('653_CTAB.*')
In [850]:
sds_646_regex = re.compile('646_SDS.*')
In [851]:
sds_377_regex = re.compile('377_SDS.*')
In [1107]:
sds_220_regex = re.compile('220_SDS.*')
In [1108]:
sds_75_regex = re.compile('75_SDS.*')
In [631]:
ctab_bilayer_systems = list(
    set( filter(bilayer_regex.match, system_names) ) \
    & set( filter( ctab_regex.match, system_names ) ) )
In [637]:
ctab_monolayer_systems = list(
    set( filter(monolayer_regex.match, system_names) ) \
    & set( filter( ctab_regex.match, system_names ) ) )
In [650]:
ctab_hemicylindrical_systems = list( # attention cylinders & hemicylinders swicthed accidentially
    set( filter(cylinders_regex.match, system_names) ) \
    & set( filter( ctab_regex.match, system_names ) ) )
In [651]:
ctab_cylindrical_systems = list( # attention cylinders & hemicylinders swicthed accidentially
    set( filter(hemicylinders_regex.match, system_names) ) \
    & set( filter( ctab_regex.match, system_names ) ) )
In [660]:
ctab_653_systems = list( set( filter( ctab_653_regex.match, system_names ) ) )
In [639]:
ctab_monolayer_systems
Out[639]:
['653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped']
In [638]:
ctab_bilayer_systems
Out[638]:
['1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped']
In [652]:
ctab_hemicylindrical_systems
Out[652]:
[]
In [654]:
ctab_cylindrical_systems
Out[654]:
['653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped']
In [661]:
ctab_653_systems
Out[661]:
['653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped']
In [862]:
system_names
Out[862]:
['1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped']
In [844]:
sds_bilayer_systems = list(
    set( filter(bilayer_regex.match, system_names) ) \
    & set( filter( sds_regex.match, system_names ) ) )
In [846]:
sds_monolayer_systems = list(
    set( filter(monolayer_regex.match, system_names) ) \
    & set( filter( sds_regex.match, system_names ) ) )
In [858]:
sds_hemicylindrical_systems = list(
    set( filter(hemicylinders_regex.match, system_names) ) \
    & set( filter( sds_regex.match, system_names ) ) )
In [859]:
sds_cylindrical_systems = list( 
    set( filter(cylinders_regex.match, system_names) ) \
    & set( filter( sds_regex.match, system_names ) ) )
In [852]:
sds_646_systems = list( set( filter( sds_646_regex.match, system_names ) ) )
In [853]:
sds_377_systems = list( set( filter( sds_377_regex.match, system_names ) ) )
In [1109]:
sds_220_systems = list( set( filter( sds_220_regex.match, system_names ) ) )
In [1110]:
sds_75_systems = list( set( filter( sds_75_regex.match, system_names ) ) )
In [1111]:
system_names
Out[1111]:
['1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped']
In [854]:
sds_monolayer_systems
Out[854]:
['646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped']
In [855]:
sds_bilayer_systems
Out[855]:
['220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped']
In [663]:
shape_labels = ['monolayer','bilayer', 'cylinders']
In [682]:
shape_labels
Out[682]:
['monolayer', 'bilayer', 'cylinders']
In [664]:
shape_label_dict = dict(zip(system_names, shape_labels))
In [699]:
def shape_label_assigner(system_name):
    if monolayer_regex.match(system_name):
        return 'monolayer'
    elif bilayer_regex.match(system_name):
        return 'bilayer'
    elif hemicylinders_regex.match(system_name) and sds_regex.match(system_name):
        return 'hemicylinder'
    elif cylinders_regex.match(system_name) and ctab_regex.match(system_name):
        return 'hemicylinder'
    else:
        return 'cylinder'
In [700]:
shape_label_dict = {
    system_name: shape_label_assigner(system_name) for system_name in system_names
}
In [701]:
shape_label_dict
Out[701]:
{'1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': 'bilayer',
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped': 'monolayer',
 '1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': 'bilayer',
 '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': 'bilayer',
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': 'monolayer',
 '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': 'bilayer',
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': 'monolayer',
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped': 'monolayer',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': 'bilayer',
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': 'monolayer',
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': 'bilayer',
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped': 'cylinder',
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': 'monolayer',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped': 'bilayer',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped': 'cylinder',
 '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped': 'monolayer',
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped': 'bilayer',
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped': 'monolayer'}
In [702]:
np.array(production_steps) * postprocessing.fs
Out[702]:
array([  5.00000000e-10,   1.00000000e-09])
In [703]:
distance_covered = 100 # rough estimate
In [704]:
rate_labels = distance_covered * postprocessing.AA / ( 
    2* np.array(production_steps) * postprocessing.fs ) # labels in m/s or nm/ns
In [705]:
rate_labels
Out[705]:
array([ 10.,   5.])
In [706]:
production_dict
Out[706]:
{500000: 'production_500000', 1000000: 'production_1000000'}
In [707]:
rate_labels_str = [ 
    r'$' + '{:>2d}'.format(int(vel)) + r' \mathrm{m} \mathrm{s}^{-1}$' \
                   for vel in rate_labels ]
In [708]:
rate_labels_str
Out[708]:
['$10 \\mathrm{m} \\mathrm{s}^{-1}$', '$ 5 \\mathrm{m} \\mathrm{s}^{-1}$']
In [709]:
rate_label_dict = dict(zip(production_steps,rate_labels_str))
In [996]:
data_tags = ['thermo', 'colvars', 'ti.pmf', 'ti.grad', 'ti.count']
fig_tags =  ['thermo', 'colvars', 'groupgroup', 'pmf' ]
In [711]:
system_selection = ctab_653_systems
In [906]:
dist_interval = slice(20,80)
In [743]:
df_dict.keys()
Out[743]:
dict_keys(['1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped', '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped', '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped', '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped', '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped', '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped', '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped', '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped', '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped', '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped', '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped', '1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped', '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped', '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped', '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped', '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped', '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped', '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped'])
In [744]:
df_dict['377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped'].keys()
Out[744]:
dict_keys([500000])

Thermo- & group interaction plots

In [1138]:
system_lst
Out[1138]:
['1107_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_hemicylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '415_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '515_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '515_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped']
In [1045]:
indenter_system_suffix = '_50Ang_stepped'
In [1049]:
original_system_lst = [ s[:-len(indenter_system_suffix)] for s in system_lst ]
In [1058]:
molecules_per_area = 1e-18/sim_df.loc[original_system_lst,'sb_area_per_sf_molecule'] # in nm**2
In [1139]:
shape_label_dict = dict( zip( system_lst, [ '${: 4.2f} \mathrm{{nm}}^{{-2}}$'.format(gamma) for gamma in molecules_per_area]))
In [1140]:
n_surfactant_regexp = re.compile('^([0-9]+)_.*')
In [1141]:
n_surfactant = [ int(n_surfactant_regexp.match(s).group(1)) for s in system_lst ]
In [1157]:
system_selection = ctab_hemicylindrical_systems
In [1154]:
system_selection = sorted(system_selection,key=lambda s: dict(zip(system_lst,n_surfactant))[s])
In [1155]:
system_selection = sorted(system_selection)
In [1158]:
system_selection
Out[1158]:
[]
In [1096]:
shape_label_dict = dict( zip( system_selection, ['bilayer', 'monolayer', 'cylinders']))
In [1131]:
shape_label_dict = dict( zip( system_selection, ['bilayer', 'hemicylinders', 'monolayer']))
In [1124]:
shape_label_dict = dict( zip( system_selection, ['bilayer','monolayer']))
In [1028]:
window = 3
In [1151]:
# plot all
i = 0
rate_fig_dict = {} # same shape, different rates
shape_fig_dict = {} # same rate, different shapes

# plots_of_interest = ''
# for system_name, steps_df_dict in df_dict.items():
for system_name in system_selection:
    steps_df_dict = df_dict[system_name]          
    for total_steps, data_df_dict in steps_df_dict.items():
        if system_name in exclude_dict and total_steps in exclude_dict[system_name]:
            continue
            
        print("{:<72s} {:>12d}".format(system_name, total_steps))
        
        if total_steps not in shape_fig_dict:
            shape_fig_dict[total_steps] = {}
            for tag in fig_tags:
                shape_fig_dict[total_steps][tag] = {}
                shape_fig_dict[total_steps][tag]['fig']  = None
                shape_fig_dict[total_steps][tag]['axes'] = None
    
        if system_name not in rate_fig_dict:
            rate_fig_dict[system_name] = {}
            for tag in fig_tags:
                rate_fig_dict[system_name][tag] = {}
                rate_fig_dict[system_name][tag]['fig']  = None
                rate_fig_dict[system_name][tag]['axes'] = None
        #for df_name, df in data_df_dict.items():
        #    if df_name 
        #    print(df_name)
        ( shape_fig_dict[total_steps]['groupgroup']['fig'],
          shape_fig_dict[total_steps]['groupgroup']['axes'] ) = \
            postprocessing.makeGroupGroupInteractionsByDistPlot( 
                data_df_dict['thermo'], 
                data_df_dict['colvars'], 
                data_df_dict['ti.pmf'],
                fig  = shape_fig_dict[total_steps]['groupgroup']['fig'],
                axes = shape_fig_dict[total_steps]['groupgroup']['axes'],
                legend_prefix = shape_label_dict[system_name], 
                interval = dist_interval, window = window,
                x_offset = - data_df_dict['dist_offset'],
                force_factor = force_conversion_factor,
                distance_label=r'Distance $ d \ \left( \mathrm{\AA} \right)$',
                force_label=r'Normal force $ F \ \left( \mathrm{nN} \right)$')

        ( rate_fig_dict[system_name]['groupgroup']['fig'],
          rate_fig_dict[system_name]['groupgroup']['axes'] ) = \
            postprocessing.makeGroupGroupInteractionsByDistPlot( 
                data_df_dict['thermo'], 
                data_df_dict['colvars'], 
                data_df_dict['ti.pmf'],
                fig  = rate_fig_dict[system_name]['groupgroup']['fig'],
                axes = rate_fig_dict[system_name]['groupgroup']['axes'],
                legend_prefix = rate_label_dict[total_steps], 
                interval = dist_interval, window = window,
                x_offset = - data_df_dict['dist_offset'],
                force_factor = force_conversion_factor,
                distance_label=r'Distance $ d \ \left( \mathrm{\AA} \right)$',
                force_label=r'Normal force $ F \ \left( \mathrm{nN} \right)$')
        i+=1
    
print("Finished after {:d} loops".format(i))
367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped             500000
653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped             500000
Finished after 2 loops
In [ ]:
 
In [1152]:
shape_fig_dict[500000]['groupgroup']['fig']
Out[1152]:
In [1068]:
rate_fig_dict.keys()
Out[1068]:
dict_keys(['75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped', '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped', '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped', '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped', '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped'])
In [ ]:
 
In [1072]:
system_selection
Out[1072]:
['75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '220_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped']
In [1073]:
rate_fig_dict['75_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped']['groupgroup']['fig']
Out[1073]:
In [1030]:
for ax in shape_fig_dict[500000]['groupgroup']['axes']:
    ax.legend().set_visible(False)
In [ ]:
 
In [717]:
rate_fig_dict['653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped']['groupgroup']['fig']
Out[717]:
In [718]:
shape_fig_dict[500000]['groupgroup']['fig']
Out[718]:
In [719]:
fig_tags
Out[719]:
['thermo', 'colvars', 'groupgroup', 'pmf']
In [753]:
fig_tags = ['indenter_forces_z', 'nonindenter_forces_z']
In [754]:
dist_interval = slice(25,80)

Netcdf force plots

In [1003]:
data_df_dict.keys()
Out[1003]:
dict_keys(['colvars', 'ti.pmf', 'ti.grad', 'ti.count', 'thermo'])
In [1004]:
# plot all
i = 0
rate_fig_dict = {} # same shape, different rates
shape_fig_dict = {} # same rate, different shapes

# plots_of_interest = ''
for system_name, steps_df_dict in df_dict.items():
    # rate_fig_dict[system_name] = {}
    # shape_fig_dict[system_name] = {}
    
    if system_name not in system_selection:
        continue
          
    for total_steps, data_df_dict in steps_df_dict.items():
        if system_name in exclude_dict and total_steps in exclude_dict[system_name]:
            continue
            
        print("{:<72s} {:>12d}".format(system_name, total_steps))
        
        if total_steps not in shape_fig_dict:
            shape_fig_dict[total_steps] = {}
            for tag in fig_tags:
                shape_fig_dict[total_steps][tag] = {}
                shape_fig_dict[total_steps][tag]['fig']  = None
                shape_fig_dict[total_steps][tag]['axes'] = None
    
#         if system_name not in rate_fig_dict:
#             rate_fig_dict[system_name] = {}
#             for tag in fig_tags:
#                 rate_fig_dict[system_name][tag] = {}
#                 rate_fig_dict[system_name][tag]['fig']  = None
#                 rate_fig_dict[system_name][tag]['axes'] = None
        
        
        ( shape_fig_dict[total_steps]['indenter_forces_z']['fig'],
          shape_fig_dict[total_steps]['indenter_forces_z']['axes'] ) = \
            postprocessing.makeVariableByDistPlot( 
                data_df_dict['indenter_forces_z'][["f_storeUnconstrainedForcesAve"]]*force_conversion_factor,
                data_df_dict['colvars'], 
                data_df_dict['ti.pmf'],
                fig  = shape_fig_dict[total_steps]['indenter_forces_z']['fig'],
                axes = shape_fig_dict[total_steps]['indenter_forces_z']['axes'],
                #legend_prefix = shape_label_dict[system_name], 
                legend = shape_label_dict[system_name],
                interval = dist_interval, window = 5,
                x_offset = data_df_dict['dist_offset'],
                x_label=r'Distance $ d \ \left( \mathrm{\AA} \right)$',
                y_label=r'Normal force $ F \ \left( \mathrm{nN} \right)$')

#         ( shape_fig_dict[total_steps]['nonindenter_forces_z']['fig'],
#           shape_fig_dict[total_steps]['nonindenter_forces_z']['axes'] ) = \
#             postprocessing.makeVariableByDistPlot( 
#                 data_df_dict['nonindenter_forces_z'][["f_storeUnconstrainedForcesAve"]], 
#                 data_df_dict['colvars'], 
#                 data_df_dict['ti.pmf'],
#                 fig  = shape_fig_dict[total_steps]['nonindenter_forces_z']['fig'],
#                 axes = shape_fig_dict[total_steps]['nonindenter_forces_z']['axes'],
#                 #legend_prefix = shape_label_dict[system_name], 
#                 legend = shape_label_dict[system_name],
#                 interval = dist_interval, window = 5,
#                 x_offset = data_df_dict['dist_offset'],
#                 x_label=r'Distance $ d \ \left( \mathrm{\AA} \right)$',
#                 y_label=r'Normal force $ F \ \left( \mathrm{nN} \ \mathrm{mol}^{-1} \right)$')
            
        #for tag in fig_tags:
        #    shape_fig_dict[total_steps][tag]['fig'].legend()
        i+=1
    
print("Finished after {:d} loops".format(i))
129_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped              500000
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-1004-4502b05dea13> in <module>()
     36           shape_fig_dict[total_steps]['indenter_forces_z']['axes'] ) = \
     37             postprocessing.makeVariableByDistPlot( 
---> 38                 data_df_dict['indenter_forces_z'][["f_storeUnconstrainedForcesAve"]]*force_conversion_factor,
     39                 data_df_dict['colvars'],
     40                 data_df_dict['ti.pmf'],

KeyError: 'indenter_forces_z'
In [832]:
label_dict = dict( zip( system_lst, system_lst))
In [895]:
ctab_653_systems
Out[895]:
['653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped']
In [896]:
system_selection = ['653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped']
In [990]:
sds_cylindrical_systems
Out[990]:
[]
In [975]:
nsds_lst = [646,75,129,377,220]
In [973]:
system_selection = sds_monolayer_systems
In [987]:
system_selection
Out[987]:
['377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped']
In [985]:
system_selection
Out[985]:
['377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped',
 '377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped']
In [ ]:
system_selection = sorted(system_selection,key=lambda s: dict(zip(sds_bilayer_systems,nsds_lst))[s])
In [979]:
sys
Out[979]:
<module 'sys' (built-in)>
In [947]:
rate_label_dict
Out[947]:
{500000: '$10 \\mathrm{m} \\mathrm{s}^{-1}$',
 1000000: '$ 5 \\mathrm{m} \\mathrm{s}^{-1}$'}
In [942]:
window = 1
In [965]:
dist_interval = slice(25,80)
In [982]:
system_selection = sds_377_systems
In [984]:
# plot all
i = 0
rate_fig_dict = {} # same shape, different rates
shape_fig_dict = {} # same rate, different shapes

# plots_of_interest = ''
# for system_name, steps_df_dict in df_dict.items():
for system_name in system_selection:
    steps_df_dict = df_dict[system_name]
    # rate_fig_dict[system_name] = {}
    # shape_fig_dict[system_name] = {}
    
    if system_name not in system_selection:
        continue
          
    for total_steps, data_df_dict in steps_df_dict.items():
        if system_name in exclude_dict and total_steps in exclude_dict[system_name]:
            continue
            
        print("{:<72s} {:>12d}".format(system_name, total_steps))
        
        if total_steps not in shape_fig_dict:
            shape_fig_dict[total_steps] = {}
            for tag in fig_tags:
                shape_fig_dict[total_steps][tag] = {}
                shape_fig_dict[total_steps][tag]['fig']  = None
                shape_fig_dict[total_steps][tag]['axes'] = None
    
        if system_name not in rate_fig_dict:
            rate_fig_dict[system_name] = {}
            for tag in fig_tags:
                rate_fig_dict[system_name][tag] = {}
                rate_fig_dict[system_name][tag]['fig']  = None
                rate_fig_dict[system_name][tag]['axes'] = None
        
        
        ( shape_fig_dict[total_steps]['indenter_forces_z']['fig'],
          shape_fig_dict[total_steps]['indenter_forces_z']['axes'] ) = \
            postprocessing.makeVariableByDistPlot( 
                data_df_dict['indenter_forces_z'][["f_storeUnconstrainedForcesAve"]]*force_conversion_factor,
                data_df_dict['colvars'], 
                data_df_dict['ti.pmf'],
                fig  = shape_fig_dict[total_steps]['indenter_forces_z']['fig'],
                axes = shape_fig_dict[total_steps]['indenter_forces_z']['axes'],
                #legend_prefix = shape_label_dict[system_name], 
                legend = label_dict[system_name],
                interval = dist_interval, window = window,
                x_offset = data_df_dict['dist_offset'],
                x_label=r'Distance $ d \ \left( \mathrm{\AA} \right)$',
                y_label=r'Normal force $ F \ \left( \mathrm{nN} \right)$')

#         ( shape_fig_dict[total_steps]['nonindenter_forces_z']['fig'],
#           shape_fig_dict[total_steps]['nonindenter_forces_z']['axes'] ) = \
#             postprocessing.makeVariableByDistPlot( 
#                 data_df_dict['nonindenter_forces_z'][["f_storeUnconstrainedForcesAve"]], 
#                 data_df_dict['colvars'], 
#                 data_df_dict['ti.pmf'],
#                 fig  = shape_fig_dict[total_steps]['nonindenter_forces_z']['fig'],
#                 axes = shape_fig_dict[total_steps]['nonindenter_forces_z']['axes'],
#                 #legend_prefix = shape_label_dict[system_name], 
#                 legend = shape_label_dict[system_name],
#                 interval = dist_interval, window = 5,
#                 x_offset = data_df_dict['dist_offset'],
#                 x_label=r'Distance $ d \ \left( \mathrm{\AA} \right)$',
#                 y_label=r'Normal force $ F \ \left( \mathrm{nN} \ \mathrm{mol}^{-1} \right)$')

        ( rate_fig_dict[system_name]['indenter_forces_z']['fig'],
          rate_fig_dict[system_name]['indenter_forces_z']['axes'] ) = \
            postprocessing.makeVariableByDistPlot( 
                data_df_dict['indenter_forces_z'][["f_storeUnconstrainedForcesAve"]]*force_conversion_factor,
                data_df_dict['colvars'], 
                data_df_dict['ti.pmf'],
                fig  = rate_fig_dict[system_name]['indenter_forces_z']['fig'],
                axes = rate_fig_dict[system_name]['indenter_forces_z']['axes'],
                #legend_prefix = shape_label_dict[system_name], 
                legend = rate_label_dict[total_steps], #label_dict[system_name],
                interval = dist_interval, window = window,
                x_offset = data_df_dict['dist_offset'],
                x_label=r'Distance $ d \ \left( \mathrm{\AA} \right)$',
                y_label=r'Normal force $ F \ \left( \mathrm{nN} \right)$')
            
        #for tag in fig_tags:
        #    shape_fig_dict[total_steps][tag]['fig'].legend()
        i+=1
    
print("Finished after {:d} loops".format(i))
377_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped              500000
377_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped                500000
Finished after 2 loops
In [914]:
ctab_653_systems
Out[914]:
['653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped',
 '653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped']
In [920]:
df_dict[ctab_653_systems[0]][500000]['dist_offset']
Out[920]:
25.961959207147274
In [919]:
df_dict[ctab_653_systems[1]][500000]['dist_offset']
Out[919]:
25.070358975210553
In [921]:
df_dict[ctab_653_systems[2]][500000]['dist_offset']
Out[921]:
26.245008260148126
In [922]:
ave_offset = np.sum( [df_dict[ctab_653_systems[i]][500000]['dist_offset'] for i in range(3) ] ) / 3
In [950]:
ave_offset
Out[950]:
25.759108814168652
In [784]:
nonindenter_force_z_sum_df.index = indenter_force_z_sum_df.index
In [ ]:
 
In [811]:
postprocessing.makeVariableByDistPlot(
    nonindenter_force_z_sum_df[['f_storeUnconstrainedForcesAve']]*force_conversion_factor, 
    colvars_traj_df, pmf_df,
    x_offset = dist_offset,
    interval=d_interval, window=1,
    x_label=r'Distance $ d \ \left( \mathrm{\AA} \right)$',
    y_label=r'Normal force $ F \ \left( \mathrm{nN} \mathrm{mol}^{-1} \right)$')
Out[811]:
(<matplotlib.figure.Figure at 0x7f44cc76a748>,
 [<matplotlib.axes._subplots.AxesSubplot at 0x7f44b81b34e0>])
In [739]:
data_df_dict.keys()
Out[739]:
dict_keys(['colvars', 'ti.pmf', 'ti.grad', 'ti.count', 'thermo'])
In [742]:
data_df_dict.keys()
Out[742]:
dict_keys(['colvars', 'ti.pmf', 'ti.grad', 'ti.count', 'thermo'])

Colvars

In [129]:
df_dict['646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped'][500000].keys()
Out[129]:
dict_keys(['colvars', 'ti.pmf', 'ti.grad', 'ti.count', 'thermo'])
In [130]:
colvars_traj_df = df_dict['646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped'][500000]['colvars']
In [132]:
pmf_df = df_dict['646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped'][500000]['ti.pmf']
In [154]:
grad_df = df_dict['646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped'][500000]['ti.grad']
In [155]:
count_df = df_dict['646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped'][500000]['ti.count']
In [133]:
fig, axes = postprocessing.makeColvarsPlots(
    colvars_traj_df, #interval=slice(5000,None), 
    legend_prefix = 'raw');
In [134]:
fig, axes = postprocessing.makeColvarsPlots(
    colvars_traj_df, #interval=slice(5000,None), 
    window = 100,
    fig = fig, axes = axes, legend_prefix = 'ave' );
In [135]:
fig
Out[135]:
In [150]:
dist_interval=slice(20,60)
In [151]:
fig, axes = postprocessing.makeColvarsPlotsByDist(
    colvars_traj_df, pmf_df, legend_prefix = 'raw',
    interval=dist_interval);
In [152]:
fig, axes = postprocessing.makeColvarsPlotsByDist(
    colvars_traj_df, pmf_df, legend_prefix = 'ave', window = 5,
    fig = fig, axes = axes, interval=dist_interval );
In [153]:
fig
Out[153]:
In [156]:
fig, axes = postprocessing.makePMEPlots(
    pmf_df, grad_df, count_df, 
    interval = dist_interval,
    legend_prefix ='raw');
In [638]:
fig, axes = postprocessing.makePMEPlots(
    pmf_df, grad_df, count_df, 
    interval = slice(40,100),
    legend_prefix ='ave', window = 5,
    fig = fig, axes = axes);
In [639]:
fig
Out[639]:

Thermo output

In [ ]:
postprocessing.read_production_thermo()
In [476]:
thermo_df = postprocessing.evaluate_production();
In [555]:
fig, axes = postprocessing.makeThermoPlotsFromDataFrame(
    thermo_df, legend_prefix = 'raw');
In [556]:
fig, axes = postprocessing.makeThermoPlotsFromDataFrame(
    thermo_df, fig = fig, axes = axes, window=50, 
    legend_prefix='ave');
In [558]:
fig
Out[558]:

Group - Group interactions

In [584]:
fig, axes = postprocessing.makeGroupGroupInteractionsPlot(thermo_df,legend_prefix='raw')
In [585]:
fig, axes = postprocessing.makeGroupGroupInteractionsPlot(
    thermo_df,legend_prefix='ave', window=50,
    fig = fig, axes = axes)
In [586]:
fig
Out[586]:
In [591]:
fig, axes = postprocessing.makeGroupGroupInteractionsByDistPlot(
    thermo_df, colvars_traj_df, pmf_df, legend_prefix = 'raw');
In [592]:
fig, axes = postprocessing.makeGroupGroupInteractionsByDistPlot(
    thermo_df, colvars_traj_df, pmf_df, legend_prefix = 'ave', window=5,
    fig = fig, axes = axes );
In [662]:
fig
Out[662]:
In [139]:
thermo_df = postprocessing.evaluate_production();
In [142]:
postprocessing.evaluate_group_group_interactions(thermo_df);
In [15]:
for dirname, dirnames, filenames in os.walk('.'):
    # print path to all subdirectories first.
    for subdirname in dirnames:
        print(os.path.join(dirname, subdirname))

    # print path to all filenames.
    for filename in filenames:
        print(os.path.join(dirname, filename))

    # Advanced usage:
    # editing the 'dirnames' list will stop os.walk() from recursing into there.
    if '.git' in dirnames:
        # don't go into any .git directories.
        dirnames.remove('.git')
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
./1298_CTAB_on_AU_111_63x36x2_monolayer_with_counterion
./515_CTAB_on_AU_111_63x36x2_bilayer_with_counterion
./653_CTAB_on_AU_111_63x36x2_inverse_monolayer_with_counterion
./367_CTAB_on_AU_111_63x36x2_cylinders_with_counterion
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion
./653_CTAB_on_AU_111_63x36x2_cylinders_with_counterion
./415_CTAB_on_AU_111_63x36x2_inverse_monolayer_with_counterion
./415_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped
./653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped
./1010_CTAB_on_AU_111_63x36x2_inverse_monolayer_with_counterion
./367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion
./367_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
./515_CTAB_on_AU_111_63x36x2_inverse_monolayer_with_counterion
./367_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion
./515_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion
./367_CTAB_on_AU_111_63x36x2_bilayer_with_counterion
./415_CTAB_on_AU_111_63x36x2_monolayer_with_counterion
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion
./515_CTAB_on_AU_111_63x36x2_cylinders_with_counterion
./415_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion
./1010_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion
./1298_CTAB_on_AU_111_63x36x2_inverse_monolayer_with_counterion
./.ipynb_checkpoints
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
./367_CTAB_on_AU_111_63x36x2_inverse_monolayer_with_counterion
./653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion
./515_CTAB_on_AU_111_63x36x2_monolayer_with_counterion
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion
./1298_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion
./Untitled.ipynb
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_cylinder_002_restart.pack
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_ioncylinder_000_restart.pack
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_packmol.pdb
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_nvtEquilibrated.lammps
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_cylinder_001_restart.pack
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_restart.pack
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen_ctrl.pdb
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_nvtEquilibration.log
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_minimization.log
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_segments.tar.gz
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_packmol.inp
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_cylinder_000_restart.pack
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen.in
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen_ctrl.psf
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen.data
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_minimized.lammps
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_packmol.pdb_FORCED
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_ionized.gro
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_ioncylinder_002_restart.pack
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_minimization_thermo.out
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_ioncylinder_001_restart.pack
./1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1298_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_nvtEquilibration_thermo.out
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/nptEquilibrated
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_minimization.log
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_minimized.lammps
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized/lmp_minimization.out
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_minimization_thermo.out
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/nptEquilibrated/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_nptEquilibrated.lammps
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/nptEquilibrated/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_nptEquilibration_thermo.out
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/nptEquilibrated/lmp_nptEquilibration.out
./1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/nptEquilibrated/1298_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_nptEquilibration.log
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/minimized
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/nptEquilibrated
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.count
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.colvars.traj
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.grad
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_thermo.out
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_mixed.nc
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production.log
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/colvars.tar.gz
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped.restart1.colvars.state
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/minimized/lmp_minimization.out
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/minimized/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_minimization_thermo.out
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/minimized/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_minimized.lammps
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/minimized/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_minimization.log
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/nptEquilibrated/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_nptEquilibrated.lammps
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/nptEquilibrated/lmp_nptEquilibration.out
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/nptEquilibrated/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_nptEquilibration_thermo.out
./1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/nptEquilibrated/1010_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_nptEquilibration.log
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/nptEquilibrated
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production.log
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/colvars.tar.gz
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_mixed.nc
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_thermo.out
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized/1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_minimized.lammps
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized/lmp_minimization.out
./1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized/1010_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_minimization_thermo.out
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./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_minimized.lammps
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_10ns_production_mixed.log
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_nvtEquilibration_thermo.out
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_nptEquilibrated.lammps
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_psfgen_ctrl.psf
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_nptEquilibration_thermo.out
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_nvtEquilibration.log
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_psfgen_ctrl.pdb
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_ionized.gro
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_packmol.inp
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_10ns_production_mixed_thermo.out
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_psfgen.in
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_packmol.pdb
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_segments.tar.gz
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_nvtEquilibrated.lammps
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_nptEquilibration.log
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_minimization.log
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/restart001/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_production_mixed.nc
./415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion/restart000/415_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_production_mixed.nc
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/restart000
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_minimized.lammps
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_nvtEquilibration_thermo.out
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen_ctrl.pdb
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_nvtEquilibrated.lammps
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_segments.tar.gz
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen_ctrl.psf
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_minimization.log
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_packmol.pdb
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen.data
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen.in
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_nvtEquilibration.log
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_ionized.gro
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_packmol.inp
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_nptEquilibration.log
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_nptEquilibrated.lammps
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_nptEquilibration_thermo.out
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_minimization_thermo.out
./415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/restart000/415_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_production_mixed.nc
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_100000
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_50000
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/nptEquilibrated
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production.log
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/colvars.tar.gz
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_mixed.nc
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_1000000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_thermo.out
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_minimization.log
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized/lmp_minimization.out
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_minimization_thermo.out
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/minimized/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_minimized.lammps
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_100000/lmp_production.out
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_100000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production.log
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_100000/colvars.tar.gz
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_100000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_mixed.nc
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_100000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_thermo.out
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_100000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_mixed.lammps
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_50000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_thermo.out
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_50000/colvars.tar.gz
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_50000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_mixed.nc
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_50000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production.log
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_50000/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_production_mixed.lammps
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/production_50000/lmp_production.out
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/nptEquilibrated/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_nptEquilibrated.lammps
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/nptEquilibrated/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_nptEquilibration.log
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/nptEquilibrated/lmp_nptEquilibration.out
./653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped/nptEquilibrated/653_CTAB_on_AU_111_63x36x2_bilayer_with_counterion_50Ang_stepped_nptEquilibration_thermo.out
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/minimized
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_100000
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_50000
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/nptEquilibrated
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_thermo.out
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/colvars.tar.gz
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production.log
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_1000000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_mixed.nc
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/minimized/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_minimization_thermo.out
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/minimized/lmp_minimization.out
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/minimized/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_minimization.log
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/minimized/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_minimized.lammps
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_100000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_mixed.lammps
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_100000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_thermo.out
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_100000/colvars.tar.gz
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_100000/lmp_production.out
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_100000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production.log
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_100000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_mixed.nc
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_50000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_mixed.lammps
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_50000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_thermo.out
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_50000/colvars.tar.gz
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_50000/lmp_production.out
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_50000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production.log
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/production_50000/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_production_mixed.nc
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/nptEquilibrated/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_nptEquilibration_thermo.out
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/nptEquilibrated/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_nptEquilibrated.lammps
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/nptEquilibrated/lmp_nptEquilibration.out
./653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped/nptEquilibrated/653_CTAB_on_AU_111_63x36x2_monolayer_with_counterion_50Ang_stepped_nptEquilibration.log
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_restart.pack
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_packmol.inp
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen.in
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen_ctrl.psf
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_minimized.lammps
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_ionized.gro
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_cylinder_000_restart.pack
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_minimization_thermo.out
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_ioncylinder_000_restart.pack
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_packmol.pdb_FORCED
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_cylinder_001_restart.pack
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_ioncylinder_001_restart.pack
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_ioncylinder_002_restart.pack
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen_ctrl.pdb
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_psfgen.data
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_packmol.pdb
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_cylinder_002_restart.pack
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_segments.tar.gz
./1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion/1010_CTAB_on_AU_111_63x36x2_cylinders_with_counterion_minimization.log
In [111]:
!cat  653_CTAB_on_AU_111_63x36x2_hemicylinders_with_counterion_50Ang_stepped.indenter_pulled.ti.pmf
#       xi            A(xi)
        20       997560.15932667
        21       997560.15932667
        22       997560.15932667
        23       997560.15932667
        24       997560.15932667
        25       997560.15932667
        26       997560.15932667
        27       997560.15932667
        28       997560.15932667
        29       997560.15932667
        30       997560.15932667
        31       997560.15932667
        32       997560.15932667
        33       997560.15932667
        34       997560.15932667
        35       997560.15932667
        36       997560.15932667
        37       997560.15932667
        38       997560.15932667
        39       997560.15932667
        40       995166.05066242
        41        992543.4926676
        42       989671.05778106
        43       986554.80492018
        44       983190.35200818
        45       979565.30376182
        46       975691.27294107
        47       971567.58012446
        48       967192.38019571
        49       962563.94676838
        50       957688.49883347
        51       952568.56341398
        52       947185.78059218
        53       941562.91682284
        54        935684.8893103
        55        929563.7058149
        56         923179.586528
        57       916557.57891403
        58       909682.30215161
        59       902562.28946854
        60       895186.66863882
        61         887560.877216
        62       879693.81472497
        63        871570.8135686
        64       863196.87022931
        65       854560.75252139
        66       845675.48392349
        67       836553.65959979
        68        827176.8971815
        69       817548.21625799
        70       807678.72998687
        71       797553.32664398
        72       787178.94294778
        73       776568.32415654
        74        765692.8681953
        75        754570.6277493
        76       743206.98832987
        77       731592.29578265
        78       719707.59307449
        79       707581.53182763
        80        695202.4813572
        81       682665.55001683
        82       670207.18896017
        83       657762.20958428
        84       645339.89352013
        85       632946.02229838
        86       620593.23343108
        87       608288.46388805
        88       596018.59088779
        89       583770.90942736
        90        571552.5839035
        91       559386.63009166
        92       547268.43150475
        93       535224.36896454
        94       523192.97806923
        95       511181.63359883
        96       499226.50159315
        97       487317.10924608
        98       475440.59832643
        99       463626.28588881
       100       451847.82748273
       101       440121.37941456
       102       428452.03756783
       103       416836.52461523
       104       405298.77594472
       105        393772.6081794
       106       382322.04691423
       107       370943.72842466
       108       359624.57505753
       109       348365.47860259
       110       337175.13909274
       111       326060.09239619
       112       315010.12563479
       113        303998.6435724
       114       293066.35123495
       115       282138.18183133
       116        271234.4609242
       117       260340.75742106
       118       249442.93781456
       119       238577.70656638
       120       227733.11945986
       121       216924.96101114
       122       206156.11515221
       123        195439.0089322
       124       184781.43024743
       125       174166.55757638
       126       163630.64824045
       127       153142.56771215
       128       142741.58009908
       129       132402.42520703
       130       122182.55777833
       131       112046.56206921
       132        102013.1319896
       133       92109.352300241
       134       82344.318984174
       135       72730.312851059
       136       63268.141822997
       137       54014.175285991
       138       44957.851931086
       139       36166.747812396
       140       28558.823576894
       141       21667.483687531
       142       16141.986526546
       143        11273.86966624
       144       7156.4051526446
       145       3869.1395994392
       146       1666.0375908836
       147                     0
       148                     0
       149                     0
       150                     0
       151                     0
       152                     0
       153                     0
       154                     0
       155                     0
       156                     0
       157                     0
       158                     0
       159                     0
       160                     0

netcdf evaluation

Forces

$ [F_{LMP}] = \frac{ \mathrm{kcal}}{ \mathrm{mol} \cdot \mathrm{\mathring{A}}} $

$ [F_{PLT}] = \mathrm{nm}$

$ \mathrm{kcal} = 4.184 \mathrm{kJ} = 4.184 \cdot 10^{3} \mathrm{J}$

$ J = N \cdot m$

$ N = J m^{-1} = \frac{ \mathrm{kcal}}{ 4.184 \cdot 10^3 \mathrm{m} } = \frac{ \mathrm{kcal}}{ 4.184 \cdot 10^{13} \mathrm{\mathring{A}} }$

$ [F_{PLT}] = \mathrm{nN} = \frac{ 10^9 \cdot N_A^{-1}}{ 4.184 \cdot 10^{13} } \frac{\mathrm{kcal}}{\mathrm{mol} \cdot \mathrm{\mathring{A}}} = \frac{ 10^{-4} \cdot N_A^{-1}}{ 4.184 } [F_{LMP}] = 0.239 \cdot 10^{-4} N_A^{-1} [F_{LMP}] $

In [314]:
system_names
Out[314]:
['646_SDS_on_AU_111_51x30x2_bilayer_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_cylinders_with_counterion_50Ang_stepped',
 '646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped']
In [159]:
system_name
Out[159]:
'646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped'
In [163]:
production_absolute_prefix = os.sep.join((
    system_absolute_prefix_dict[system_name],
    production_dict[500000]))
In [164]:
production_absolute_prefix
Out[164]:
'/work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000'
In [165]:
netcdf_glob_pattern = os.sep.join((
    production_absolute_prefix, '*.nc'))
In [475]:
netcdf_glob_pattern
Out[475]:
'/work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/*.nc'
In [167]:
netcdf = glob(netcdf_glob_pattern)[0]
In [282]:
netcdf
Out[282]:
'/work/ws/nemo/fr_jh1130-201708-0/jobs/lmplab/sds/201810/sys/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped/production_500000/646_SDS_on_AU_111_51x30x2_monolayer_with_counterion_50Ang_stepped_production_mixed.nc'
In [239]:
postprocessing.sds_t2n_array
Out[239]:
array([ 0,  1,  1,  6,  6,  8,  8, 16,  1,  8, 11, 79], dtype=uint64)
In [240]:
tmp_traj = NetCDFTrajectory(
    netcdf, 'r', 
    types_to_numbers = list( postprocessing.sds_t2n_array ),
                        keep_open=True )
In [241]:
len(tmp_traj)
Out[241]:
551
In [287]:
f1 = tmp_traj[0]
In [286]:
f2 = tmp_traj[-1]

select groups

In [290]:
solid_selection = (
    f.get_atomic_numbers() == ase.data.atomic_numbers['Au'])
In [293]:
indenter_selection = (
    solid_selection & (f.get_positions()[:,2] > 20) )
In [300]:
np.count_nonzero(indenter_selection)
Out[300]:
3541
In [301]:
tmp_traj[0][ indenter_selection ]
Out[301]:
Atoms(symbols='Au3541', pbc=True, cell=[147.53766532813174, 150.29686998263395, 169.97117870911075], f_storeAnteSHAKEForces=..., f_storeAnteSHAKEForcesAve=..., f_storeAnteStatForces=..., f_storeAnteStatForcesAve=..., f_storeUnconstrainedForces=..., f_storeUnconstrainedForcesAve=..., forces=..., masses=..., mol=...)
In [302]:
tmp_traj[-1][ indenter_selection]
Out[302]:
Atoms(symbols='Au3541', pbc=True, cell=[146.28029880699086, 147.31903563329237, 174.42972818989477], f_storeAnteSHAKEForces=..., f_storeAnteSHAKEForcesAve=..., f_storeAnteStatForces=..., f_storeAnteStatForcesAve=..., f_storeUnconstrainedForces=..., f_storeUnconstrainedForcesAve=..., forces=..., masses=..., mol=...)
In [306]:
len(tmp_traj[0][ solid_selection ]) # 21901
Out[306]:
21901
In [307]:
len(tmp_traj[0][ indenter_selection ]) # 3541
Out[307]:
3541
In [308]:
tmp_traj[0][ indenter_selection ].get_positions().max(axis=0)
Out[308]:
array([ 125.9885788 ,  127.94010925,  153.44935608])
In [309]:
for key in force_keys:
    force_sum_dict[key] = f_indenter.arrays[key].sum(axis=0)
In [273]:
force_keys = [
    'forces', 
    'f_storeAnteSHAKEForces', 
    'f_storeAnteStatForces', 
    'f_storeUnconstrainedForces', 
    'f_storeAnteSHAKEForcesAve', 
    'f_storeAnteStatForcesAve', 
    'f_storeUnconstrainedForcesAve' ]
In [310]:
force_sum_dict = { key: [] for key in force_keys }
In [ ]:
df = pd.DataFrame()
In [361]:
tmp_traj[100][indenter_selection].arrays.keys()
Out[361]:
dict_keys(['numbers', 'positions', 'masses', 'mol', 'forces', 'f_storeAnteSHAKEForces', 'f_storeAnteStatForces', 'f_storeUnconstrainedForces', 'f_storeAnteSHAKEForcesAve', 'f_storeAnteStatForcesAve', 'f_storeUnconstrainedForcesAve'])
In [351]:
# sum forces on all indenter atoms for all frames
indenter_force_sum_dict = { key: [] for key in force_keys }
nonindenter_force_sum_dict = { key: [] for key in force_keys }
for key in force_keys:    
    indenter_force_sum_dict[key] = np.array(
        [ f[indenter_selection].arrays[key].sum(axis=0) 
             for f in tmp_traj ] )
    nonindenter_force_sum_dict[key] = np.array(
        [ f[~indenter_selection].arrays[key].sum(axis=0) 
             for f in tmp_traj ] )
In [352]:
data_prefix = '/work/ws/nemo/fr_jh1130-201708-0/jobs/doc/md/surfactants/data/forces'
In [353]:
indenter_force_z_sum_dict = { key: value[:,2] for key, value 
                        in indenter_force_sum_dict.items() }
In [354]:
nonindenter_force_z_sum_dict = { key: value[:,2] for key, value 
                        in nonindenter_force_sum_dict.items() }
In [355]:
indenter_force_z_sum_df = pd.DataFrame.from_dict(indenter_force_z_sum_dict, dtype=float)
In [356]:
nonindenter_force_z_sum_df = pd.DataFrame.from_dict(nonindenter_force_z_sum_dict, dtype=float)
In [398]:
production_steps = 500000
In [399]:
production_dict[production_steps]
Out[399]:
'production_500000'
In [400]:
system_prefix = system_name + '_' + production_dict[production_steps]
In [389]:
indenter_z_forces_json_name = system_prefix + '_indenter_z_forces.json'
In [391]:
nonindenter_z_forces_json_name = system_prefix + '_nonindenter_z_forces.json'
In [382]:
# indenter_z_forces_csv_name = system_name + '_' + production_dict[500000] + '_indenter_z_forces.csv'
In [386]:
indenter_force_z_sum_df.to_json(
    os.sep.join((data_prefix, indenter_z_forces_json_name)),  orient='index')
In [392]:
nonindenter_force_z_sum_df.to_json(
    os.sep.join((data_prefix, nonindenter_z_forces_json_name)),  orient='index')
In [ ]:
 
In [ ]:
 
In [404]:
pmf_df = df_dict[system_name][production_steps]['ti.pmf']
In [407]:
colvars_traj_df = df_dict[system_name][production_steps]['colvars']
In [416]:
thermo_df = df_dict[system_name][production_steps]['thermo']
In [450]:
# initial apex position at frame 0:
apex_z0 = tmp_traj[0][indenter_selection].get_positions()[:,2].min()
In [453]:
# initial substrate surface position at frame 0:
surface_z0 = tmp_traj[0][solid_selection & ~indenter_selection].get_positions()[:,2].max()
In [454]:
extents_dist_0 = apex_z0 - surface_z0
In [456]:
extents_dist_0
Out[456]:
98.177323341369629
In [461]:
com_com_dist_0 = colvars_traj_df.loc[0,'com_com_dist_z']
In [462]:
com_com_dist_0
Out[462]:
127.232566602432
In [463]:
dist_offset = com_com_dist_0 - extents_dist_0
In [464]:
dist_offset
Out[464]:
29.055243261062373
In [406]:
df_dict[system_name][production_steps].keys()
Out[406]:
dict_keys(['colvars', 'ti.pmf', 'ti.grad', 'ti.count', 'thermo'])
In [420]:
len(thermo_df.index)
Out[420]:
55001
In [429]:
thermo_df.index
Out[429]:
Int64Index([     0,     10,     20,     30,     40,     50,     60,     70,
                80,     90,
            ...
            549910, 549920, 549930, 549940, 549950, 549960, 549970, 549980,
            549990, 550000],
           dtype='int64', name='Step', length=55001)
In [428]:
len(colvars_traj_df)
Out[428]:
550001
In [421]:
colvar_freq = 1 # every step
In [422]:
netcdf_freq = 1e-3 # every 1000 steps
In [434]:
indenter_force_z_sum_df.set_index(
    (indenter_force_z_sum_df.index/netcdf_freq*colvar_freq).astype(int),
    inplace=True )
In [438]:
colvars_traj_df_dist_column = "com_com_dist_z"
In [440]:
#colvars_traj_df[colvars_traj_df_dist_column]
In [468]:
d_interval = slice(25,80)
In [812]:
postprocessing.makeVariableByDistPlot(
    indenter_force_z_sum_df[['f_storeUnconstrainedForcesAve']]*force_conversion_factor, 
    colvars_traj_df, pmf_df,
    x_offset = dist_offset,
    interval=d_interval, window=1,
    x_label=r'Distance $ d \ \left( \mathrm{\AA} \right)$',
    y_label=r'Normal force $ F \ \left( \mathrm{nN} \mathrm{mol}^{-1} \right)$')
Out[812]:
(<matplotlib.figure.Figure at 0x7f4517d807b8>,
 [<matplotlib.axes._subplots.AxesSubplot at 0x7f4517969c88>])
In [445]:
indenter_force_z_sum_df
Out[445]:
f_storeAnteSHAKEForces f_storeAnteSHAKEForcesAve f_storeAnteStatForces f_storeAnteStatForcesAve f_storeUnconstrainedForces f_storeUnconstrainedForcesAve forces
0 0.0 0.0 0.0 0.0 73.958130 0.000000 0.0
1000 0.0 0.0 0.0 0.0 289.104187 171.355240 0.0
2000 0.0 0.0 0.0 0.0 -124.337997 -29.272726 0.0
3000 0.0 0.0 0.0 0.0 952.008972 644.509521 0.0
4000 0.0 0.0 0.0 0.0 941.272217 961.847900 0.0
5000 0.0 0.0 0.0 0.0 795.886902 766.855591 0.0
6000 0.0 0.0 0.0 0.0 296.076477 502.439636 0.0
7000 0.0 0.0 0.0 0.0 369.026215 334.348236 0.0
8000 0.0 0.0 0.0 0.0 200.233337 378.965607 0.0
9000 0.0 0.0 0.0 0.0 250.446350 374.582581 0.0
10000 0.0 0.0 0.0 0.0 165.093094 278.261017 0.0
11000 0.0 0.0 0.0 0.0 -137.109604 177.699768 0.0
12000 0.0 0.0 0.0 0.0 178.077271 85.003044 0.0
13000 0.0 0.0 0.0 0.0 168.095612 73.940742 0.0
14000 0.0 0.0 0.0 0.0 -59.295563 25.406065 0.0
15000 0.0 0.0 0.0 0.0 -409.678040 -22.691568 0.0
16000 0.0 0.0 0.0 0.0 -122.354652 -84.475708 0.0
17000 0.0 0.0 0.0 0.0 35.546455 -77.136917 0.0
18000 0.0 0.0 0.0 0.0 -38.477428 -128.536758 0.0
19000 0.0 0.0 0.0 0.0 -149.094528 -128.107819 0.0
20000 0.0 0.0 0.0 0.0 -244.567993 -123.367928 0.0
21000 0.0 0.0 0.0 0.0 -50.754711 -178.388962 0.0
22000 0.0 0.0 0.0 0.0 -320.525696 -137.675537 0.0
23000 0.0 0.0 0.0 0.0 -268.271332 -129.132095 0.0
24000 0.0 0.0 0.0 0.0 -184.733917 -128.252579 0.0
25000 0.0 0.0 0.0 0.0 84.908333 -105.924385 0.0
26000 0.0 0.0 0.0 0.0 -164.355225 -101.981628 0.0
27000 0.0 0.0 0.0 0.0 175.719864 -90.983917 0.0
28000 0.0 0.0 0.0 0.0 321.733307 -22.558500 0.0
29000 0.0 0.0 0.0 0.0 -112.205505 -39.825924 0.0
... ... ... ... ... ... ... ...
521000 0.0 0.0 0.0 0.0 2097.895264 1867.624268 0.0
522000 0.0 0.0 0.0 0.0 1714.888916 1793.459473 0.0
523000 0.0 0.0 0.0 0.0 1682.859131 1838.773315 0.0
524000 0.0 0.0 0.0 0.0 1985.445312 1752.428833 0.0
525000 0.0 0.0 0.0 0.0 1548.846924 1739.419189 0.0
526000 0.0 0.0 0.0 0.0 1835.891846 1700.451660 0.0
527000 0.0 0.0 0.0 0.0 1733.260254 1722.260986 0.0
528000 0.0 0.0 0.0 0.0 1775.456299 1716.454834 0.0
529000 0.0 0.0 0.0 0.0 1673.797485 1723.109009 0.0
530000 0.0 0.0 0.0 0.0 1998.820923 1700.264038 0.0
531000 0.0 0.0 0.0 0.0 1429.226685 1636.405518 0.0
532000 0.0 0.0 0.0 0.0 1819.824341 1528.203613 0.0
533000 0.0 0.0 0.0 0.0 1448.620728 1571.840698 0.0
534000 0.0 0.0 0.0 0.0 1592.135620 1577.874023 0.0
535000 0.0 0.0 0.0 0.0 1390.668701 1534.669067 0.0
536000 0.0 0.0 0.0 0.0 1682.058594 1588.570435 0.0
537000 0.0 0.0 0.0 0.0 1261.268188 1597.866211 0.0
538000 0.0 0.0 0.0 0.0 1597.030640 1574.392822 0.0
539000 0.0 0.0 0.0 0.0 1686.156372 1547.179810 0.0
540000 0.0 0.0 0.0 0.0 1546.776367 1570.629028 0.0
541000 0.0 0.0 0.0 0.0 1242.286743 1505.408081 0.0
542000 0.0 0.0 0.0 0.0 1479.711060 1541.082397 0.0
543000 0.0 0.0 0.0 0.0 1495.226562 1491.236694 0.0
544000 0.0 0.0 0.0 0.0 1382.185669 1464.515747 0.0
545000 0.0 0.0 0.0 0.0 1782.494629 1451.337524 0.0
546000 0.0 0.0 0.0 0.0 1673.258057 1490.495972 0.0
547000 0.0 0.0 0.0 0.0 1444.129761 1498.001709 0.0
548000 0.0 0.0 0.0 0.0 1266.342896 1498.866455 0.0
549000 0.0 0.0 0.0 0.0 1310.006348 1510.401978 0.0
550000 0.0 0.0 0.0 0.0 1399.237793 1520.988770 0.0

551 rows × 7 columns

In [366]:
interval = slice(100,400)
In [813]:
plt.plot(indenter_force_z_sum_df['f_storeUnconstrainedForcesAve']*force_conversion_factor)
plt.plot(nonindenter_force_z_sum_df['f_storeUnconstrainedForcesAve']*force_conversion_factor)
Out[813]:
[<matplotlib.lines.Line2D at 0x7f45191415c0>]
In [367]:
plt.plot(indenter_force_z_sum_df['f_storeUnconstrainedForcesAve'][interval]*force_conversion_factor_per_mole)
plt.plot(nonindenter_force_z_sum_df['f_storeUnconstrainedForcesAve'][interval]*force_conversion_factor_per_mole)
Out[367]:
[<matplotlib.lines.Line2D at 0x7f4519529240>]
In [ ]:
'f_storeAnteSHAKEForcesAve', 
'f_storeAnteStatForcesAve', 
'f_storeUnconstrainedForcesAve' 
In [362]:
plt.plot(indenter_force_z_sum_df['f_storeAnteStatForcesAve']*force_conversion_factor_per_mole)
plt.plot(nonindenter_force_z_sum_df['f_storeAnteStatForcesAve']*force_conversion_factor_per_mole)
Out[362]:
[<matplotlib.lines.Line2D at 0x7f451923f390>]
In [368]:
plt.plot(indenter_force_z_sum_df['f_storeAnteStatForcesAve'][interval]*force_conversion_factor_per_mole)
plt.plot(nonindenter_force_z_sum_df['f_storeAnteStatForcesAve'][interval]*force_conversion_factor_per_mole)
Out[368]:
[<matplotlib.lines.Line2D at 0x7f45196cbb70>]
In [369]:
plt.plot(indenter_force_z_sum_df['f_storeAnteSHAKEForcesAve']*force_conversion_factor_per_mole)
plt.plot(nonindenter_force_z_sum_df['f_storeAnteSHAKEForcesAve']*force_conversion_factor_per_mole)
Out[369]:
[<matplotlib.lines.Line2D at 0x7f45196eb7b8>]
In [370]:
plt.plot(indenter_force_z_sum_df['f_storeAnteSHAKEForcesAve'][interval]*force_conversion_factor_per_mole)
plt.plot(nonindenter_force_z_sum_df['f_storeAnteSHAKEForcesAve'][interval]*force_conversion_factor_per_mole)
Out[370]:
[<matplotlib.lines.Line2D at 0x7f45197b8f60>]
In [371]:
plt.plot(indenter_force_z_sum_df['forces'][interval]*force_conversion_factor_per_mole)
plt.plot(nonindenter_force_z_sum_df['forces'][interval]*force_conversion_factor_per_mole)
Out[371]:
[<matplotlib.lines.Line2D at 0x7f4519ac9dd8>]
In [331]:
force_sum_dict['f_storeUnconstrainedForcesAve'][:,2]
Out[331]:
551
In [ ]:
# 3541 in indenter, 18360 in substrate
In [264]:
f_indenter.arrays.keys()
Out[264]:
dict_keys(['numbers', 'positions', 'masses', 'mol', 'forces', 'f_storeAnteSHAKEForces', 'f_storeAnteStatForces', 'f_storeUnconstrainedForces', 'f_storeAnteSHAKEForcesAve', 'f_storeAnteStatForcesAve', 'f_storeUnconstrainedForcesAve'])
In [279]:
force_sum_dict = {}
In [280]:
for key in force_keys:
    force_sum_dict[key] = f_indenter.arrays[key].sum(axis=0)
In [ ]:
 
In [281]:
force_sum_dict
Out[281]:
{'f_storeAnteSHAKEForces': masked_array(data = [0.0 0.0 0.0],
              mask = [False False False],
        fill_value = 1e+20),
 'f_storeAnteSHAKEForcesAve': masked_array(data = [0.0 0.0 0.0],
              mask = [False False False],
        fill_value = 1e+20),
 'f_storeAnteStatForces': masked_array(data = [0.0 0.0 0.0],
              mask = [False False False],
        fill_value = 1e+20),
 'f_storeAnteStatForcesAve': masked_array(data = [0.0 0.0 0.0],
              mask = [False False False],
        fill_value = 1e+20),
 'f_storeUnconstrainedForces': masked_array(data = [-18.106060028076172 -35.41413497924805 73.9581298828125],
              mask = [False False False],
        fill_value = 1e+20),
 'f_storeUnconstrainedForcesAve': masked_array(data = [0.0 0.0 0.0],
              mask = [False False False],
        fill_value = 1e+20),
 'forces': masked_array(data = [0.0 0.0 0.0],
              mask = [False False False],
        fill_value = 1e+20)}
In [180]:
NetCDFTrajectory?
In [181]:
traj = ase.io.read(netcdf,index=0,format='netcdftrajectory')
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-181-fbf2e17f155e> in <module>()
----> 1 traj = ase.io.read(netcdf,index=0,format='netcdftrajectory')

/work/ws/nemo/fr_lp1029-IMTEK_SIMULATION-0/local_modules/ase/3.15.0/lib/python3.6/site-packages/ase-3.15.0-py3.6.egg/ase/io/formats.py in read(filename, index, format, parallel, **kwargs)
    420         index = -1
    421     format = format or filetype(filename)
--> 422     io = get_ioformat(format)
    423     if isinstance(index, (slice, basestring)):
    424         return list(_iread(filename, index, format, io, parallel=parallel,

/work/ws/nemo/fr_lp1029-IMTEK_SIMULATION-0/local_modules/ase/3.15.0/lib/python3.6/site-packages/ase-3.15.0-py3.6.egg/ase/io/formats.py in get_ioformat(format)
    199 def get_ioformat(format):
    200     """Initialize and return IOFormat tuple."""
--> 201     initialize(format)
    202     return ioformats[format]
    203 

/work/ws/nemo/fr_lp1029-IMTEK_SIMULATION-0/local_modules/ase/3.15.0/lib/python3.6/site-packages/ase-3.15.0-py3.6.egg/ase/io/formats.py in initialize(format)
    190         read = functools.partial(wrap_read_function, read)
    191     if not read and not write:
--> 192         raise ValueError('File format not recognized: ' + format)
    193     code = all_formats[format][1]
    194     single = code[0] == '1'

ValueError: File format not recognized: netcdftrajectory
In [182]:
ase.__version__
Out[182]:
'3.15.0'
In [491]:
data_df
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-491-38ce564c9fb1> in <module>()
----> 1 data_df

NameError: name 'data_df' is not defined
In [ ]: